Tangled Roots

An ancient finger bone recently landed a genetic sucker punch on scientists studying human evolution. DNA extracted from this tiny fossil, unearthed in Siberia’s Denisova Cave, unveiled a humanlike population that interbred with people in East Asia at least 44,000 years ago. Denisovans supplied nearly 5 percent of the genes of native groups now living in Australia, New Guinea and on several nearby islands.

That molecular shocker followed a revelation that the genetic instruction books of people from Australia to the Americas contain a roughly 2.5 percent contribution from Neandertals, modern humans’ evolutionary cousins that died out around 30,000 years ago. Pulling the DNA shades up on ancient human dalliances with Neandertals and closely related Denisovans has sparked a scientific consensus that members of mobile human groups interbred with closely related populations in the Homo genus during the Stone Age.

“The question is no longer ‘When did ancient populations such as Neandertals go extinct?’ but ‘What happened to those populations and to modern humans as a result of interbreeding?’ ” says anthropologist John Hawks of the University of Wisconsin–Madison.

Clear signs of interbreeding have left archaeologists and other students of the Stone Age scrambling to revisit existing ideas about Homo sapiens’ evolutionary past. A dominant theory holding that humans evolved in Africa and left on neat one-way routes to Asia and Europe has to be revised. Instead, these ancient people must have followed a tangled web of paths taking them to other continents and sometimes reversing course. During these travels, humans encountered Neandertals, Denisovans and probably other humanlike populations that were already traipsing interconnected avenues through Asia and Europe.

With this new picture, two underdog models of human history have gotten new life. Both favor population intersections during extensive travels across ancient landscapes. But one maintains that moving populations were separate species, while a second regards Neandertals and Denisovans as two of possibly many subspecies gradually incorporated into a uniform, modern version of H. sapiens.

New genetic evidence and more artifacts that tell Asia’s side of the evolutionary story may offer the only chance for settling, or at least narrowing, the dispute.

So long, Eve

Only a few years ago, Neandertals had a scientific reputation as evolutionary also-rans. The seeds of their destruction were sown around 1.7 million years ago when Homo erectus — an early Homo species — trekked from Africa into Asia. This hardy species, the first human ancestor to leave Africa, survived until perhaps 200,000 years ago and may have evolved into small-bodied Homo floresiensis, or hobbits, in Indonesia.

An H. erectus descendant, Homo heidelbergensis, originated at least 600,000 years ago — possibly in Africa — and spread across that continent, southern Europe and southern Asia. Between 300,000 and 400,000 years ago, H. heidelbergensis evolved into Homo neanderthalensis — Neandertals — in West Asia. By 130,000 years ago, H. heidelbergensis in Africa had become H. sapiens, the humans whose descendants now envelop the globe.

Then the evolutionary hammer came down. Beetle-browed, slope-faced Neandertals bit the dust because they got outcompeted by H. sapiens leaving Africa along a series of uninterrupted paths starting around 60,000 years ago. Competition for the same resources created an intense rivalry that discouraged interbreeding, many researchers claimed. Neandertals lost the survival sweepstakes and died out around 30,000 years ago. H. sapiens pressed on, ultimately reaching South America by about 14,000 years ago.

A famous 1987 study of mitochondrial DNA, which is passed from mothers to their offspring, spawned this idea — known as the out-of-Africa or recent African origin model. Analyses of mitochondrial DNA sequences in people around the world suggested that a small number of mothers lucky enough to have had a fertile chain of female offspring up to the present lived in Africa 200,000 years ago. These ancient ladies received the collective nickname Mitochondrial Eve.

Reports in the mid-1990s that Neandertal mitochondrial DNA markedly differs from that of humans were taken by out-of-Africa proponents as further evidence against Stone Age interbreeding.

But investigators now realize that fast-evolving changes in this brand of human DNA could have erased signs of interbreeding. Evidence from DNA in cell nuclei, which is inherited from both parents and evolves relatively slowly, suggests up to 4 percent of DNA in modern Asians and Europeans was inherited from Neandertals (SN: 6/5/10, p. 5). What’s more, nuclear DNA retrieved from Stone Age fossils in places cold enough to preserve it gossips about long-ago liaisons between people and another evolutionary relative, the Denisovans (SN: 1/15/11, p. 10).

Telltale DNA suggests that many ancient groups migrated back and forth to new areas. Small in numbers, those groups spent generations evolving distinctive physical characteristics in relative isolation before running into other wanderers and interbreeding with them. In this way, various genetic traits got passed among closely related groups over vast territories.

“We were naïve to think that humans just marched out of Africa, killed some Neandertals and populated the world,” says archaeologist John Shea of Stony Brook University in New York.

Remodeling the past

As a key architect of the formerly dominant out-of-Africa model of human evolution, anthropologist Chris Stringer of the Natural History Museum in London was caught off guard by reports of ancient interbreeding. Stringer now accepts that genetic intermingling occurred, but he sees that activity as secondary to genetic evolution that had already largely molded H. sapiens in Africa.

In his new book Lone Survivors, Stringer dubs his modified perspective a “mostly out of Africa” model. The modified version provides for limited interbreeding before Neandertals and Denisovans died out, but Stringer proposes that these species’ genes offered no major survival advantages to H. sapiens.

More than 90 percent of people’s genes today now derive from African H. sapiens, Stringer says. As H. sapiens left Africa and spread across the globe starting 60,000 years ago, they encountered and sometimes interbred with other offshoots of H. heidelbergensis, including Neandertals and Denisovans. Stringer suspects that occasional interbreeding with ancient humanlike species had a limited effect on the anatomy of H. sapiens. Closely related species of baboons and other primates interbreed where population ranges overlap without losing their biological identities, he says.

While surviving Neandertal and Denisovan genes caused Stringer to add a dash of interbreeding to his out-of-Africa model, those same DNA revelations delighted theorists who have long regarded interbreeding as a key influence on human evolution. In their view, mobile groups of various Homo species — or perhaps of one geographically variable species of ancient H. sapiens — must have crossed paths and mated enough to rock each other’s genomes.

“I jumped up and down when the Neandertal genome came out,” says anthropologist Fred Smith of Illinois State University in Normal.

For more than 20 years, Smith and anthropologist Erik Trinkaus of Washington University in St. Louis have championed a minority view known as the assimilation model. It holds that H. sapiens originated in Africa but interbred fairly often with Neandertals and other evolutionary relatives. An increasing number of genetic changes to human DNA over the last 10,000 years, stimulated by mating across much larger populations than in the Stone Age, has erased evidence of far more than a 2.5 percent Neandertal genetic heritage, Smith suspects.

In this view, ancient humans and Neandertals shared a mosaic of skeletal traits despite belonging to separate species. Although researchers have found no genetic evidence of a human impact on Neandertals, Neandertal skulls and jaws from Croatia’s Vindija Cave dating to between 38,000 and 32,000 years ago exhibit a shift toward smaller facial features like those of ancient European H. sapiens, Smith reported in April in Portland, Ore., at the American Association of Physical Anthropologists’ annual meeting. People reached Europe by at least 40,000 years ago and could have changed the look of Vindija Neandertals via interbreeding.

Traces of interbreeding on Vindija fossils fit a scenario in which African H. sapiens could reproduce with any other Homo population, including those often regarded as different species, says anthropologist John Relethford of the State University of New York at Oneonta.

Hundreds, perhaps thousands, of human and humanlike groups moved across Africa, Asia and Europe during the Stone Age, Relethford says. Some groups mated with others, some kept their distance and others attacked competitors. An unknown number of mobile bands died out.

“We’re trying to reconstruct a big evolutionary grid from a small number of data points,” Relethford says.

While assimilationists see different Homo species moving along that grid and sometimes interbreeding, another perspective lumps Neandertals, Denisovans and others into a single species that evolved on different continents beginning nearly 2 million years ago. Far-flung, physically distinctive human groups interbred enough during their travels to keep H. sapiens genetically glued together, these researchers propose.

Anthropologist Milford Wolpoff of the University of Michigan in Ann Arbor champions this perspective, known since the 1930s as multiregional evolution. H. sapiens arose almost 2 million years ago as an African population that many anthropologists mistakenly label as H. erectus, Wolpoff says. Those ancient Africans rapidly moved into Asia and Europe, spawning a series of anatomical variations on the H. sapiens theme.

Mating across H. sapiens subspecies promoted intercontinental unity, and occurred often enough that advantageous genes in one population spread to all others. In this way, a trait such as a prominent chin, for example, could have appeared in Africa before becoming widespread, whereas other traits, including a high forehead, could have radiated from an Asian homeland.

A population explosion that began 50,000 years ago and has accelerated in the last 10,000 years, accompanied by adults living progressively longer, prompted so much breeding across populations that human races disappeared altogether, Wolpoff asserts. People now encompass a uniform species with more minor regional variations in skin color, stature and other characteristics.

“I think humanity included Neandertals, although many disagree,” says Wisconsin’s Hawks.

Genetic rescue

Putting together the genetic bits and pieces will be a complex task. In a recent twist, a team led by Sarah Tishkoff of the University of Pennsylvania reports that three hunter-gatherer groups currently living in Africa carry genetic signatures that may have been produced by interbreeding with a now-extinct African Homo species 30,000 to 70,000 years ago. But without any genetic material from this mysterious Stone Age species, it’s hard to make any firm claims, Tishkoff and colleagues report in the Aug. 3 Cell.

A fuller picture of human evolutionary history clearly awaits further ancient DNA evidence. Research teams around the world are now competing to obtain fingernail-sized bone samples from museum-held Homo fossils. Scientists hope to build a genetic record of human ancestors comparable to the existing fossil record.

A group led by evolutionary geneticist Johannes Krause of the University of Tübingen, Germany, is trying to remove and reassemble nuclear DNA from the bones of roughly 20,000-year-old people in Europe. If successful, that effort will provide the first look at whether Stone Age humans carried more Neandertal genes than people today do. “It’s a completely open question whether more interbreeding occurred in the past than what we’ve found so far,” Krause says.

Preliminary evidence that Neandertals and Denisovans passed beneficial genes to H. sapiens suggests interbreeding was not only common but also crucial to survival. A 2011 investigation led by Stanford University geneticist Peter Parham concluded that several genes involved in the body’s disease-fighting immune system spread from Neandertals and Denisovans to humans and are now common in some parts of Asia. Further support for genetically advantageous mating across species would be bad news for Stringer’s mostly out-of-Africa model.

Other researchers comparing genetic contributions in people around the world today are getting a handle on whether Denisovan and Neandertal genes caught on in some populations more than others.

Krause and his colleagues recently found Denisovan DNA in Australian Aborigines and natives of several Oceanic islands but not in residents of mainland Southeast Asia. Denisovans may have gone from Southeast Asia to Oceanic islands where they interbred with people who eventually reached Australia on canoes or rafts, proposes Krause, who formerly worked with a team that analyzed the genetic blueprint of Neandertals and Denisovans. The finding would explain why native groups now living in Australia, New Guinea and nearby islands display slightly different amounts and types of Denisovan DNA.

Southeast Asians may, however, possess roughly 1 percent Denisovan ancestry, say evolutionary geneticists Pontus Skoglund and Mattias Jakobsson of Uppsala University in Sweden. A small genetic connection between Southeast Asians and Denisovans emerged when comparing the genetic instruction books of a larger sample of living people with the ancient Siberian genome, the researchers reported in a 2011 paper.

If that finding holds up, then Denisovans interbred unevenly with different groups of ancient humans. So did Neandertals, but on a geographically grander scale, says Hawks. By consulting data that other researchers posted on an open-access website, he has compared Neandertal DNA with genomes from about 1,000 individuals living in different parts of the world.

Small differences in Neandertal ancestry appear in people from different populations, Hawks reported at the physical anthropology meeting. He believes that his findings are consistent with multi­regional evolution: Physically distinctive groups of H. sapiens occasionally expanded their ranges and sometimes mated when they crossed paths, leaving an uneven mark on ensuing generations. A supporter of the mostly out-of-Africa approach would probably treat Hawks’ findings as regional blips in what were minimal genetic exchanges.

Europeans carry an average of about 2.5 percent Neandertal DNA, while the Chinese carry 3 percent, Hawks reported. And slightly more Neandertal DNA appears in northern Chinese than in southern Chinese. Africans possess an average of less than 1 percent Neandertal ancestry. Regardless of exactly how much interbreeding occurred during the Stone Age, Neandertals seem to have left an uneven genetic mark.

Going East

Ongoing investigations of fossils and stone tools, especially in Asia, will have their own story to tell. Numerous long-distance treks from Africa to Asia by some of the earliest toolmakers now appear undeniable. A growing number of archaeological sites, especially in China, document the presence in East Asia of teardrop-shaped hand axes made by H. erectus starting 1.7 million years ago, says Harvard University archaeologist Ofer Bar-Yosef. H. erectus fossils and tools date to the same time on the Indonesian island of Java.

New finds show that Neandertals, like H. sapiens, also went on plenty of intercontinental road trips, so the two species could have tangoed over tens of millions of square kilometers. Artifacts recently discovered in China resemble tools associated with Neandertals in Europe and West Asia, Bar-Yosef says. Neandertals aggressively expanded their territory eastward beginning perhaps 75,000 years ago, before humans had left Africa in significant numbers, he and Anna Belfer-Cohen of Hebrew University in Jerusalem propose in an upcoming Quaternary International.

Trinkaus also sees signs that thick-boned, relatively large Stone Age people who lived more than 50,000 years ago, a group of archaic H. sapiens, interbred fairly often with Neandertals in what’s now North China. Archaic human fossils from that region, mainly described in Chinese publications, look like Neandertals in some respects. Trinkaus and his colleagues have also reported that a 100,000-year-old human jaw and two associated teeth found at South China’s Zhiren Cave display a mix of archaic and anatomically modern traits.

Some researchers argue that the meeting of biologically related species in ancient East Asia was also a meeting of equal minds. Implements created by both species range from simple flakes struck off stones to finely chiseled blades, Shea says. Homo populations apparently adapted toolmaking to environmental conditions rather than crafting increasingly complex tools over time. Contrary to conventional archaeological thinking, no tool style distinguishes Neandertals from H. sapiens, Shea argues.

His scenario suggests that sophisticated thinking needed for manufacturing diverse toolkits emerged 200,000 years ago or more in both species. That’s a prospect welcomed by assimilation and multiregional theorists alike. An opposing view — congenial to mostly out-of-Africa advocates — holds that H. sapiens alone experienced a major mental leap between 70,000 and 50,000 years ago.

No one yet knows whether Asia harbors a mother lode of stones, bones and ancient DNA capable of untangling H. sapiens’ mental and physical evolution, or the movements of myriad ancient groups. For now, Asia’s Stone Age is as enigmatic as the tangled roots of its human inhabitants.

“Ten years ago, we would not have expected the extent of the mystery that has emerged,” Hawks says.