An artist’s vision of a Neanderthal and her baby. If the Neanderthal lived 47,000 to 65,000 years ago, her baby might have been the result of breeding with a human. Image: mharrsch/Flickr

Two years ago the analysis of the Neanderthal genome revealed modern humans carry Neanderthal DNA, implying our ancestors mated with Neanderthals at some point in the past. Scientists only found genetic traces of Neanderthals in non-African people, leading to the conclusion that Neanderthal-human matings must have occurred as modern humans left Africa and populated the rest of the world. A new paper (PDF) posted on arXiv.org puts a date on those matings: 47,000 to 65,000 years ago—a time that does indeed correspond with human migrations out of Africa.

Sriram Sankararaman of Harvard Medical School and colleagues—including Svante Pääbo of Germany’s Max Planck Institute for Evolutionary Anthropology and Harvard’s David Reich—investigated the timing of the matings in part to verify that the trysts even happened at all. That’s because there’s an alternative explanation for why up to 4 percent of non-African human DNA looks like Neanderthal DNA. It’s possible, the researchers explain, that the ancestral species that gave rise to both humans and Neanderthals had a genetically subdivided population—in other words, genetic variation wasn’t evenly distributed across the species. Under that scenario, Neanderthals and the modern humans that left Africa might have independently inherited similar DNA from a part of the divided ancestral population that didn’t contribute genetic material to modern African populations. (Another paper published this week, in Proceedings of the National Academy of Sciences, considers this scenario.)

To determine what really happened, Sankararaman’s team looked at rates of genetic change to estimate when Neanderthals and humans last exchanged genes. If the shared DNA was due to interbreeding, the team expected to find a date less than 100,000 years ago—some time after humans left Africa. But if it was the result of sharing a common ancestor, they expected a date older than 230,000 years ago, approximately when Neanderthals and modern humans split from each other. The team’s findings support the interbreeding scenario: 47,000 to 65,000 years ago.

Neanderthals aren’t the only archaic species that may have contributed to the modern human gene pool. Denisovans, known from only a tooth and a finger bone, left a genetic mark in people living in Melanesia and Southeast Asia. And recent genetic evidence suggests that some ancient African populations mated with an unidentified, now-extinct hominid species that lived in Africa.

So far, our knowledge of Neanderthal and Denisovan genetics comes from only a few individuals, so our understanding of interspecies mating is likely to change as more Neanderthal and Denisovan DNA is analyzed.

(H/T John Hawks)

The skull of Australopithecus sediba. Picture by Brett Eloff, courtesy of Lee Berger and the University of the Witwatersrand

For this last Hominid Hunting post of 2011, I reviewed recent human evolution research highlights to come up with my picks for the top 10 hominid discoveries of the year. While genetic breakthroughs have hogged the spotlight the past couple of years, good old-fashioned fossil and archaeological finds were front and center in 2011.

10. Earliest Modern Humans in Europe: Paleoanthropologists believe modern humans (Homo sapiens) came to Europe about 43,000 years ago. This date is based on the age of sophisticated stone tools, not human fossils. This year two teams dated European fossils that are in line with the age of the tools: A human upper jaw discovered in southern England in 1927 was dated to  44,000 years ago, and two molars unearthed in Italy were dated to 45,000 years ago. These fossils are the oldest known human remains on the continent.

9. The Arches of Australopithecus afarensis: There’s no doubt that Lucy and her species, Australopithecus afarensis, walked upright. But the degree to which these hominids walked on the ground has been debated. The discovery of a 3.2-million-year-old foot bone confirmed that Lucy and her kind had arched feet and therefore probably walked much like modern people. The researchers who studied the fossil say it indicates Australopithecus afarensis no longer needed to spend much time in the treetops; however, other researchers disagree, saying hominids at this time were still good tree climbers.

8. World’s Earliest Mattress: In a rock shelter in South Africa, archaeologists uncovered a 77,000-year-old mattress composed of thin layers of sedges and grasses, predating all other known mattresses by 50,000 years. Early humans knew how to keep the bed bugs out; the bedding was stuffed with leaves from the Cape Laurel tree (Cryptocarya woodii), which release chemicals known to kill mosquitos and other bugs.

7. Neanderthal Mountaineers: Neanderthals evolved many traits to deal with the cold; for example, their short limbs helped them conserve heat. A mathematical analysis revealed that short limbs may have also helped Neanderthals walk more efficiently in mountainous terrains. Specifically, the fact that Neanderthals had shorter shins relative to their thighs meant they didn’t need to lift their legs as high while walking uphill, compared to modern people with longer legs. “For a given step length, they [needed] to put in less effort,” said lead research Ryan Higgins of Johns Hopkins University.

6. The First Art Studio: Archaeologists working in South Africa’s Blombos Cave discovered early humans had a knack for chemistry. In a 100,000-year-old workshop, they found all of the raw materials needed to make paint, as well as abalone shells used as storage containers—evidence that our ancestors were capable of long-term planning at this time.

5. Australopithecine Females Strayed, Males Stayed Close to Home: In many monkey species, when males reach adolescence, they leave their home to search for a new group, probably as a way to avoid breeding with their female relatives. In chimpanzees and some humans, the opposite occurs: Females move away. Now it appears that australopithecines followed the chimp/human pattern. Researchers studied the composition of strontium isotopes found in the teeth of members of Australopithecus africanus and Paranthropus robustus. An individual consumes strontium through food and it is taken up by the teeth during childhood. Because the isotopes (different forms of the element) in plants and animals vary by geology and location, strontium can be used as a proxy for an individual’s location before adulthood. In the study, the researchers discovered that large individuals, presumably males, tended to have strontium isotope ratios typical of the area where the fossils were found; smaller individuals, or females, had non-local strontium isotope ratios, indicating they had moved into the area as adults.

4. Confirmation of Pre-Clovis People in North America: Since the 1930s, archaeologists have thought the Clovis people, known for their fluted projectile points, were the first people to arrive in the New World, about 13,000 years ago. But in recent years there have been hints that someone else got to North America first. The discovery of more than 15,000 stone artifacts in central Texas, dating to between 13,200 and 15,500 years ago, confirmed those suspicions. Corroborating evidence came from Washington State, where a mastodon rib containing a projectile point was dated this year to 13,800 years ago.

3. Denisovans Left A Mark in Modern DNA: The Denisovans lived in Eurasia sometime between 30,000 and 50,000 years ago. Scientists don’t know what they looked like; the only evidence of this extinct hominid group is DNA extracted from a bone fragment retrieved from a cave in Siberia. But this year, several studies revealed the mysterious population bred with several lineages of modern humans; people native to Southeast Asia, Australia, Melanesia, Polynesia and elsewhere in Oceania carry Denisovan DNA.

2. Out of Africa and Into Arabia: Traditionally, paleoanthropologists have thought modern humans left Africa through the Sinai Peninsula and into the Levant. But some researchers suggest our ancestors took a more southerly route, across the Red Sea and into southern Arabia. This year, several studies provided evidence pointing to this exit strategy. First, a team reported the discovery of 125,000-year-old stone tools in the United Arab Emirates. The researchers suggested humans ventured into Arabia when sea level was lower, making a trip across the Red Sea easier. (Geologists later verified the climate would have been just right at this time.) No fossils were found with the tools, but the scientists concluded they belonged to modern humans rather than Neanderthals or some other contemporaneous hominid. Another study this year complemented the finding: Paleoanthropologists also found stone tools, dating to 106,000 years ago, in Oman. The researchers say the artifacts match tools of the Nubian Complex, which are found only in the Horn of Africa. This connection implies the makers of those African tools, most likely modern humans, made the migration into Oman.

1. Australopithecus sediba, Candidate for Homo Ancestor: Last year, scientists announced the discovery of a new hominid species from South Africa’s Cradle of Humankind—Australopithecus sediba. This year, the researchers announced the results of an in-depth analysis of the 1.97-million-year-old species. They say a mix of australopithecine and Homo-like traits make Australopithecus sediba, or a species very similar to it, a possible direct ancestor of our own genus, Homo.

Neanderthals’ successful adaptation to climate change may have contributed to their extinction by leading to more interactions with humans. Image courtesy of Flickr user e_monk

A popular explanation for the disappearance of Neanderthals is that modern humans were superior, evolutionarily speaking. Our ancestors were smarter and more technologically advanced. When they left Africa and populated the rest of the world, the Neanderthals didn’t stand a chance.

But what if Neanderthals went extinct in part because they were too successful? New research published in the journal Human Ecology demonstrates how that’s possible. By adapting their behavior to the challenges of climate change and expanding their ranges, Neanderthals may have set up the circumstances that led to their demise.

Neanderthals emerged in Europe and West Asia by 200,000 years ago. Their close cousins, Homo sapiens, arrived in that territory sometime between 50,000 and 40,000 years ago. Within a few tens of thousands of years, Neanderthals were gone. The timing of our arrival in Eurasia and the Neanderthal extinction has led paleoanthropologists to conclude the two events are related.

Archaeologist Michael Barton of Arizona State University and his colleagues developed a new approach to studying the Neanderthal extinction, by looking at changes in land-use patterns in both Neanderthals and modern humans. They first examined 167 archaeological assemblages from across western Eurasia, from Spain to Jordan, and as far north as Romania. All of these sites date to the Late Pleistocene, 128,000 to 11,500 years ago. The team identified which species lived at which sites based on the type of artifacts; Neanderthals and humans made distinct types of stone tools.

At the beginning of the Late Pleistocene, the team discovered, both Neanderthals and modern humans tended to be nomadic, moving their camps from site to site to utilize different resources in different places. As climate became more unstable and unpredictable over time, it was harder to find resources, so both species changed their behavior: They began to travel over a larger geographic area. But instead of moving to new sites more frequently and lugging all of their stuff across greater distances, they maintained more permanent base camps and took longer, more targeted hunting and foraging trips, returning home with their bounty.

These different hunting-and-gathering strategies left their mark in the archaeological record. When Neanderthals or humans moved their camps more frequently, they tended to repair and use the same tools over and over again because it was easier to carry around fewer tools and recycle them than to bring along raw tool-making materials everywhere they went. Therefore, in archaeological sites that record nomadic behavior, archaeologists find more stone tools that have been reworked and fewer stone tools overall compared to sites that were used as more permanent base camps, where researchers find an abundance of stone tools that show little sign of being reused.

Finding that this change in behavior correlates with climate change is fascinating in its own right, but there’s another implication that relates to the question of the Neanderthal extinction. Because both humans and Neanderthals started to stray farther and farther from home to find food, they had more opportunities to come into contact with each other—more chances for mating.

In other types of animals, the researchers note, species sometimes go extinct due to breeding with closely related species, or hybridization. If one species has a larger population than the other, the less numerous species will sort of blend into the larger species. As more and more interbreeding occurs, the smaller population will eventually disappear. This may be what happened to Neanderthals, according to two population models that Barton and his colleagues developed. Under these scenarios, humans didn’t have to be better adapted to the environment (physically or culturally) than Neanderthals to win out—they just had to be more numerous. “In one sense,” the researchers write in their report, “we could say that their extinction was the result of Late Pleistocene globalization.”

Of course, it is possible that humans were more numerous and had evolutionary advantages over Neanderthals. That’s a question that requires more research and more sophisticated models. But it’s interesting to think that the Neanderthals may have sealed their fate by adapting their ranging behaviors to the changing climates of the Pleistocene. In that sense, they may have been too successful for their own good.

The molar tooth of a Denisovan. Image courtesy of David Reich et al., Nature

It’s weird to think that tens of thousands of years ago, humans were mating with different species—but they were. That’s what DNA analyses tell us. When the Neanderthal genome was sequenced in 2010, it showed that as much as 1 to 4 percent of the DNA of non-Africans might have been inherited from Neanderthals. (Given that no African populations are known to have Neanderthal DNA, the matings must have occurred as modern humans moved into Europe and Asia). Scientists also announced last year that our ancestors had mated with another extinct species, and this week, more evidence is showing how widespread that interbreeding was.

We know little about this extinct species. In fact, we don’t even have a scientific name for it; for now, the group is simply known as the Denisovans. The Denisovans were discovered after a group of scientists led by Johannes Krause, now at Tübingen University in Germany, analyzed DNA extracted from the tip of a child’s finger bone. The bone was found in 2008 in Denisova Cave in the Altai Mountains of Siberia and was dated to between 30,000 and 50,000 years ago. At that time, you’d expect to find either modern humans or Neanderthals living in Eurasia. But the finger bone’s DNA didn’t match human DNA or Neanderthal DNA. Some other kind of hominid must have also been living in the region.

A subsequent study of Denisovan DNA, in Nature, further analyzed the finger bone’s DNA and DNA from an adult molar tooth also found in Denisova Cave. Based on the physical characteristics of the tooth, it didn’t appear to be from a human or a Neanderthal, and the DNA was similar to that from the finger. David Reich of Harvard University and his colleagues furthermore compared Denisovan DNA with modern human DNA and concluded that as much as 5 percent of the DNA of people living in Melanesia could be from Denisovans—evidence of more interbreeding. Another study confirmed that Australian aborigines, Polynesians and other people of Oceania also had a Denisovan heritage. Now it appears that Southeast Asians do as well. This week Pontus Skoglunda and Mattias Jakobsson, both of Uppsala University in Sweden, reported in PNAS that Denisovan DNA may account for about 1 percent of modern Southeast Asian DNA.

The idea that our ancestors mated with other species may not be too shocking. Species today will mate with other closely related species if they come across each other in nature (or captivity). This occurs among olive baboons and hamadryas baboons that have overlapping ranges in Ethiopia. The idea probably seems surprising because it’s hard to imagine we once shared the planet with beings so similar to us. What was it like to meet other human-like individuals who weren’t quite human?

The story of our past inter-species matings is far from complete. We still don’t know who the Denisovans really were. Today, the fragment of the finger bone and the molar tooth are the sole fossils that scientists have assigned to the group. It’s impossible to say what physical features distinguished the species. But it is possible we’ve already found other Denisovan fossils. Denisovans could belong to a species whose DNA we’ve never been able to analyze, such as Homo heidelbergensis. And there are some hominid fossils in China that are hard to fit into any of the known species. If we could read their DNA, perhaps it would reveal they were Denisovans, too.