Sometime between three million and two million years ago, perhaps on a primeval savanna in Africa, our ancestors became recognizably human. For more than a million years their australopithecine predecessors—Lucy and her kind, who walked upright like us yet still possessed the stubby legs, tree-climbing hands and small brains of their ape forebearers—had thrived in and around the continent's forests and woodlands. But their world was changing. Shifting climate favored the spread of open grasslands, and the early australopithecines gave rise to new lineages. One of these offshoots evolved long legs, toolmaking hands and an enormous brain. This was our genus, Homo, the primate that would rule the planet.

For decades paleoanthropologists have combed remote corners of Africa on hand and knee for fossils of Homo's earliest representatives, seeking to understand the details of how our genus rose to prominence. Their efforts have brought only modest gains—a jawbone here, a handful of teeth there. Most of the recovered fossils instead belong to either ancestral australopithecines or later members of Homo—creatures too advanced to illuminate the order in which our distinctive traits arose or the selective pressures that fostered their emergence. Specimens older than two million years with multiple skeletal elements preserved that could reveal how the Homo body plan came together eluded discovery. Scientists' best guess is that the transition occurred in East Africa, where the oldest fossils attributed to Homo have turned up, and that Homo's hallmark characteristics allowed it to incorporate more meat into its diet—a rich source of calories in an environment where fruits and nuts had become scarce. But with so little evidence to go on, the origin of our genus has remained as mysterious as ever.

Lee Berger thinks he has found a big piece of the puzzle. A paleoanthropologist at the University of the Witwatersrand in Johannesburg, South Africa, he recently discovered a trove of fossils that he and his team believe could revolutionize researchers' understanding of Homo's roots. In the white-walled confines of room 210 at the university's Institute for Human Evolution, he watches as Bernard Wood of George Washington University paces in front of the four plastic cases that have been removed from their fireproof safe and placed on a table clothed in royal blue velvet. The foam-lined cases are open, revealing the nearly two-million-year-old fossils inside. One holds pelvis and leg bones. Another contains ribs and vertebrae. A third displays arm bones and a clavicle. And a fourth houses a skull. On a counter opposite the table, more cases hold a second partial skeleton, including a nearly complete hand.

Wood, a highly influential figure in the field, pauses in front of the skull and leans in for a closer look. He strokes his beard as he considers the dainty teeth, the grapefruit-size braincase. Straightening back up, he shakes his head. “I'm not often at a loss for words,” he says slowly, “but wow. Just wow.”

Berger grins. He has seen this reaction before. Since he unveiled the finds in 2010, scientists from all over the world have been flocking to his lab to gawk at the breathtaking fossils. Based on the unique anatomical package the skeletons present, Berger and his team assigned the remains to a new species, Australopithecus sediba. They furthermore propose that the combination of primitive Australopithecus traits and advanced Homo traits evident in the bones qualifies the species for a privileged place on the family tree: as the ancestor of Homo. The stakes are high. If Berger is right, paleoanthropologists will have to completely rethink where, when and how Homo got its start—and what it means to be human in the first place.

The Road Not Taken

In the middle of the rock-strewn dirt road that winds through the John Nash Nature Reserve, Berger brings the Jeep to a halt and points to a smaller road that branches right. For 17 years he had made the 40-kilometer trip northwest from Johannesburg to the 9,000-hectare parcel of privately owned wilderness and driven past this turnoff, continuing along the main road, past the resident giraffes and warthogs and wildebeests, to a cave he was excavating just a few kilometers away called Gladysvale. In 1948 American paleontologists Frank Peabody and Charles Camp came to this area to look for fossils of hominins (modern humans and their extinct relatives) on the advice of famed South African paleontologist Robert Broom, who had found such fossils in the caves of Sterkfontein and Swartkrans, eight kilometers away. Peabody suspected that Broom had intentionally sent them on a wild goose chase, so unimpressed was he with the sites here. Little did Berger or the expeditioners before him know that had they only followed this smaller path—one of several miners' tracks used in the early 1900s to cart the limestone that built Johannesburg from quarries out to the main road—they would have made the discovery of a lifetime.

Berger, now 46 years old, never imagined he would find something like A. sediba. Although he thought Homo might have had roots in South Africa instead of East Africa, he knew the odds of making a big find were slim. Hominin fossils are extremely rare, so “you don't have any expectations,” he reflects. What is more, he was focused on the so-called Cradle of Humankind, an already intensively explored region whose caves had long been yielding australopithecines generally considered to be more distantly related to Homo than the East African australopithecines seemed to be. And so Berger continued to toil at Gladysvale day after day, year after year. Because he found little in the way of hominins among the millions of animal fossils there, he busied himself with another goal: dating the site. A critical problem with interpreting the South African hominin fossils was that scientists had not yet figured out how to reliably determine how old they were. In East Africa, hominin fossils come from sediments sandwiched between layers of volcanic ash that blanketed the landscape during long-ago eruptions. Geologists can ascertain how old an ash layer is by analyzing its chemical “fingerprint.” A fossil that originates from a layer of sediment that sits in between two volcanic ashes is thus intermediate in age between those two ashes. The cave sites in the Cradle of Humankind lack volcanic ashes, but through his 17 years of trial and error at Gladysvale, Berger and his colleagues hit on techniques that circumvented the problem.

Those techniques would soon come in very handy. On August 1, 2008, while surveying the reserve for potential new fossil sites in the area that he had identified using Google Earth, Berger turned right on the miners' track he had passed by for 17 years and followed it to a three- by four-meter hole in the ground blasted by the miners. Eyeballing the site, he found a handful of animal fossils—enough to warrant a trip back for a closer look. He returned on August 15 with his then nine-year-old son, Matthew, and dog, Tau. Matthew took off into the bush after Tau, and within minutes he shouted to his father that he had found a fossil. Berger doubted it was anything important—probably just an antelope bone—but in a show of fatherly support, he made his way over to inspect the find. There, protruding from a dark hunk of rock nestled in the tall grass by the corpse of a lightning-struck tree, was the tip of a collarbone.

As soon as Berger laid eyes on it, he knew it belonged to a hominin. In the months that followed he found more of the clavicle's owner, along with another partial skeleton, 20 meters away in the miners' pit. To date, Berger and his team have recovered more than 220 bones of A. sediba from the site—more than all the known early Homo bones combined. He christened the site Malapa, meaning “homestead” in the local Sesotho language. Using the approaches honed at Gladysvale, the geologists on Berger's team would later date the remains with remarkable precision to 1.977 million years ago, give or take 2,000 years.

A Patchwork Predecessor

That the malapa fossils include so many body parts is important because it means they can offer unique insights into the order in which key Homo traits appeared. And what they show very clearly is that quintessentially human features did not necessarily evolve as a package deal, as was thought. Take the pelvis and the brain, for example. Conventional wisdom holds that the broad, flat pelvis of australopithecines evolved into the bowl-shaped pelvis seen in the bigger-brained Homo to allow delivery of babies with larger heads. Yet A. sediba has a Homo-like pelvis with a broad birth canal in conjunction with a teeny brain—just 420 cubic centimeters, a third of the size of our own brain. This combination shows brain expansion was not driving the metamorphosis of the pelvis in A. sediba's lineage.

Not only do the A. sediba fossils mingle old and new versions of general features, such as brain size and pelvis shape, but the pattern repeats at deeper levels, like an evolutionary fractal. Analysis of the interior of the young male's braincase shows that the brain, while small, possessed an expanded frontal region, indicating an advanced reorganization of gray matter; the adult female's upper limb pairs a long arm—a primitive holdover from a tree-dwelling ancestor—with short, straight fingers adapted to making and using tools (although the muscle markings on the bones attest to powerful, apelike grasping capabilities). In some instances, the juxtaposition of old and new is so improbable that had the bones not been found joined together, researchers would have interpreted them as belonging to entirely different creatures. The foot, for instance, combines a heel bone like an ancient ape's with an anklebone like Homo's, according to Malapa team member Bernard Zipfel of the University of the Witwatersrand. It is as if evolution was playing Mr. Potato Head, as Berger puts it.

The extreme mosaicism evident in A. sediba, Berger says, should be a lesson to paleoanthropologists. Had he found any number of its bones in isolation, he would have classified them differently. Based on the pelvis, he could have called it Homo erectus. The arm alone suggests an ape. The anklebone is a match for a modern human's. And like the blind men studying the individual parts of the elephant, he would have been wrong. “Sediba shows that one can no longer assign isolated bones to a genus,” Berger asserts. That means, in his view, finds such as a 2.3-million-year-old upper jaw from Hadar, Ethiopia, that has been held up as the earliest trace of Homo cannot safely be assumed to have belonged to the Homo line.

Taking that jaw out of the running would make A. sediba older than any of the well-dated Homo fossils but still younger than A. afarensis, putting it in pole position for the immediate ancestor of the genus, Berger's team contends. Furthermore, considering A. sediba's advanced features, the researchers propose that it could be specifically ancestral to H. erectus (a portion of which is considered by some to be a different species called Homo ergaster). Thus, instead of the traditional view in which A. afarensis begat Homo habilis, which begat H. erectus, he submits that Australopithecus africanus is the likely ancestor of A. sediba, which spawned H. erectus.

If so, that arrangement would relegate H. habilis to a dead-end side branch of the human family tree. It might even kick A. afarensis—long considered the ancestor of all later hominins, including A. africanus and Homo—to the evolutionary curb, too. Berger points out that A. sediba's heel is more primitive than that of A. afarensis, indicating that A. sediba either underwent an evolutionary reversal toward a more primitive heel or that it descended from a different lineage than the one that includes A. afarensis and A. africanus—one that has yet to be discovered.

“In the South, we have a saying: ‘You dance with the girl you brought,’” quips Berger, who grew up on a farm in Sylvania, Ga. “And that is what paleoanthropologists have been doing” in trying to piece together the origin of Homo from the fossils that have turned up in East Africa. “Now we have to recognize there is more potential out there,” he states. Maybe the East Side story of human origins is wrong. The traditional view of South Africa's oldest hominin fossils is that they represent a separate evolutionary experiment that ultimately fizzled out. A. sediba could turn the tables and reveal, in South Africa, another lineage, the one that ultimately gave rise to humankind as we know it (indeed, sediba is the Sesotho word for “fountain” or “wellspring”).

William Kimbel of Arizona State University, who led the team that found the 2.3-million-year-old jawbone in Ethiopia, is having none of it. The idea that one needs a skeleton to classify a specimen is a “nonsensical argument,” he retorts. The key is to find pieces of anatomy that contain diagnostic traits, he says, and the Hadar jaw has features clearly linking it to Homo, such as the parabolic shape formed by its tooth rows. Kimbel, who has seen the Malapa fossils but not studied them in depth, finds their Homo-like traits intriguing, although he is not sure what to make of them. He scoffs at the suggestion that they are directly ancestral to H. erectus, however. “I don't see how a taxon with a few characteristics that look like Homo in South Africa can be the ancestor [of Homo] when there's something in East Africa that is clearly Homo 300,000 years earlier,” he declares, referring to the jaw.

Kimbel is not alone in rejecting the argument for A. sediba as the rootstock of Homo. “There are too many things that do not fit, particularly the dates and geography,” comments Meave Leakey of the Turkana Basin Institute in Kenya, whose own research has focused on fossils from East Africa. “It is much more likely that the South African hominins are a separate radiation that took place in the south of the continent.”

René Bobe of George Washington University says that if the A. sediba remains were older—say, around 2.5 million years old—they might make for a plausible Homo ancestor. But at 1.977 million years old, they are just too primitive in their overall form to be ancestral to fossils from Kenya's Lake Turkana region that are just a tad younger yet have many more indisputable Homo traits. Berger counters that A. sediba almost certainly existed as a species before the Malapa individuals. Bobe and others maintain that such information is not currently known. “Paleoanthropologists tend to think of the fossils they find as being in a key position within the [hominin] phylogenetic tree, and in many cases that's unlikely to be the situation,” Bobe observes. From a statistical standpoint, “if you have [hominin] populations distributed across Africa, evolving in complex ways, why would the one you find be the ancestor?”

Berger has found a sympathetic ear in Wood, who says Berger is “absolutely right” that A. sediba demonstrates that isolated bones do not predict what the rest of the animal looks like. A. sediba shows that the combinations of traits evident from previous fossil discoveries do not exhaust the possibilities, Wood remarks. But he does not endorse the suggestion that A. sediba is the ancestor of Homo. “There are not many characters linking it to Homo,” he notes, and A. sediba may have evolved those traits independently from the Homo lineage. “I just think sediba has got too much to do in order to evolve into [erectus],” Wood says.

Resolution of the issue of where A. sediba belongs in our family tree is hampered by the lack of a clear definition of the genus Homo. Coming up with one, however, is a taller order than it might seem. With so few specimens from the transition period, and most of them being scraps, identifying those features that first distinguished Homo from its australopithecine forebearers—those traits that made us truly human—has proved challenging. The skeletons from Malapa expose just how vexing the situation is: they are so much more complete than any early Homo specimen that it is very difficult to compare them with anything. “Sediba may force us to come up with a definition,” Berger says.

All in the Details

Whatever the position of the Malapa fossils in the family tree, they are poised to provide researchers with the most detailed portrait yet of an early hominin species, in part because they make up multiple individuals. In addition to the juvenile male and the adult female, the two most complete specimens, Berger's team has collected bones representing another four individuals, including a baby. Populations are incredibly rare in the human fossil record, and the individuals at Malapa have the added benefit of peerless preservation. Hominin bones that virtually never survive the ravages of deep time have turned up here: a paper-thin shoulder blade, the delicate sliver that is the first rib, pea-size finger bones, vertebrae with spiny projections intact. And a number of bones that were previously known only from fragments are complete.

Before the discovery of Malapa, paleoanthropologists did not have a single complete arm from an early hominin, meaning that the limb lengths that are used to reconstruct such essential behaviors as locomotion are estimates. Even Lucy—the most complete hominin of such antiquity back when she was found in 1974—is missing significant chunks of her arm and leg bones. In the adult female from Malapa, in contrast, virtually the entire upper limb is preserved—from shoulder blade to hand. Only the very last digits of some of her fingers and some wristbones are missing, and Berger expects to find those—and the rest of the bones of both skeletons—when he begins systematically excavating the site. (Thus far the team has collected only bones visible from the surface.) In fact, some of the missing bones of the young male may have already turned up. In July, Berger announced that CT scanning of a large rock from the site revealed a number of bones inside, including parts of a lower jaw and possibly a complete femur. Together the Malapa fossils will enable researchers to reconstruct how A. sediba matured, how it moved around the landscape, and how members of the population differed from one another.

It is not only the bones that promise to furnish vital clues to our newfound relative's way of life. Malapa has also yielded some other materials that could literally flesh out researchers' understanding of A. sediba. Paleontologists have long thought that during the fossilization process, all of an organism's organic components—such as skin, hair, organs, and so forth—are lost to decomposition, leaving behind only mineralized bone. But when Berger saw a CT scan of the skull of the young male, he noticed a place on the crown where there appeared to be an air space between the surface of the fossil and the contour of the actual bone. Examining the spot more closely, he observed a distinctive pattern on the surface that looked like the structural components of skin. He is now conducting extensive tests to determine whether the odd-looking patch on the male's crown and another on the female's chin are in fact skin.

Preserved skin, if confirmed as such, could reveal A. sediba's coloring and the density and patterning of its hair. Such evidence could also show the distribution of sweat glands—information that would provide insights into how well the species was able to regulate its body temperature, which in turn would have affected how active it was. Sweat glands could additionally offer clues to brain evolution: an effective means of keeping cool was a prerequisite for the emergence of large brain size—a trademark characteristic of Homo—because brains are temperature-sensitive. And if organic material is present, Berger might even be able to obtain DNA from the remains. Currently the oldest hominin DNA to have been sequenced is 100,000-year-old DNA from a Neandertal. But because the preservation conditions at Malapa were apparently exceptional, Berger has some hope of getting genetic information from the much older A. sediba specimens. In that event, scientists might be able to determine whether the adult female and young male really were mother and son, as has been suggested, and how, if at all, the other hominins at the site fit in. Moreover, such a discovery would prompt researchers at other early hominin sites to test for DNA, which, if successful, could settle debates over how the various hominin species were related.

Preservation of organic remains would be a first in hominin paleontology, and the Malapa team knows it will need extraordinary evidence to persuade the research community of such a claim. Yet similar claims have been made for organic material from dinosaur bones, and those are tens of millions of years older than the Malapa fossils. Organic preservation in hominin assemblages might even be fairly common, Berger suggests—it is just that no one ever thought to look for it.

Another thing no one thought to look for in a hominin this old? Tartar. The surfaces of the young male's molar teeth bear dark brown stains. Fossil preparators typically clean off the teeth when readying hominin remains for study. But Berger realized that the stains were actually the same gunk we modern humans fend off with toothbrushes and pilgrimages to the dentist. Analyses of the stains, together with studies of the tooth chemistry and wear marks, revealed that A. sediba had a surprising diet.

In a review paper published in Science in October 2011, Peter S. Ungar of the University of Arkansas and Matt Sponheimer of the University of Colorado at Boulder observed that recent analyses have hinted at unexpected dietary diversity. Studies of what early humans ate have looked at carbon isotope ratios in teeth, which can indicate whether an animal dined on so-called C3 plants, such as trees and shrubs; C4 plants, such as certain grasses and sedges; or some combination thereof—or, in the case of carnivorous species, preyed on animals that ate those plants. Whereas Ardipithecus ramidus, one of the earliest putative hominins, dined primarily on C3 foods, as savanna chimpanzees do, other early African hominins appear to have eaten a mix of C3 and C4 foods. One species, Paranthropus robustus, even ate a mostly C4 diet, as Thure Cerling of the University of Utah and his colleagues reported in June 2011 in the Proceedings of the National Academy of Sciences USA.

Analyses of A. sediba's teeth add another facet to this diversity. In a paper published online by Nature in June, Berger, Amanda Henry of the Max Planck Institute for Evolutionary Anthropology in Leipzig and their colleagues reported that the tooth chemistry of the two most complete individuals from the site indicated a diet heavy in C3 foods. This result came as a surprise, not only because other hominins that lived around this time relied more heavily on C4 foods but because paleoecological evidence indicates that C4 plants dominated the Malapa environment. The tartar results only deepened the enigma. The team studied silica crystals called phytoliths that are embedded in the tartar. Phytoliths come from plants, and some make species-specific forms of the crystals. Studies of these phytoliths can thus reveal exactly which kinds of plants an animal ate just before it died. A. sediba apparently supped on a wide variety of plant foods, including bark—not an item researchers expected to find on an early hominin menu. The wear pattern on the teeth, meanwhile, is consistent with the consumption of some hard foods shortly before death.

Taken together, the diet findings suggest to the researchers that A. sediba foraged for C3 foods in forests surrounded by C4 grasslands. The bark evidence could indicate that the hominins were under stress because other primates are known to eat bark when fruit and other high-quality plant foods are not available. Could the C3 signature indicate that these hominins ate animals that ate C3 plants? A taste for animal flesh could fit with the hominin's small teeth, which are typically associated with a higher-quality diet, as well as its dexterous hand, which would have been well suited to making and wielding stone tools for processing meat.

End of Days

The final days of the Malapa hominins appear to have been grim ones. Possible drought conditions may have made water hard to come by. Berger suspects that the hominins, desperate for a drink, may have tried to climb down into the then 30- to 50-meter-deep underground cavern at Malapa to access a shallow pool and, in so doing, tumbled to their deaths. Perhaps the boy fell in first, and the adult female—maybe his mother—tried to rescue him only to fall in herself. A menagerie of other beasts, from antelopes to zebras, met the same fate.

Intriguingly, geologic evidence from the site indicates that the fossil assemblage at Malapa formed right around the same time that the earth was undergoing a geomagnetic reversal—a mysterious event in which the planet's polarity flips and magnetic north becomes magnetic south. The timing raises the question of whether the reversal somehow played a role in the demise of these creatures.

Scientists know very little about why reversals occur and whether they precipitate environmental change. Some geologists have suggested that these events could conceivably wreak ecological havoc. As one of the only places in the world that has a terrestrial record of a reversal and a collection of fossils from the same time, Malapa could offer rare insights into what happens when the planet's poles trade places.

Other evidence might throw additional light on their deaths. The fossilized bones of a pregnant antelope and her fetus from Malapa could help scientists pinpoint the time of year that the hominins died to within a couple of weeks: antelopes give birth within a very narrow interval in the spring, and analysis of the fetus should allow researchers to figure out how far along the antelope was before she died. Meanwhile traces of maggots and carrion beetles that set on the hominins after death could reveal how long the bodies were exposed before the cave's flowing sediments buried them.

In a sense, the work on A. sediba has only just begun. “You're walking all over hominin fossils,” Berger tells visitors to Malapa on an austral spring morning in late November 2011. They are standing on the rocky ground between the tree where Matthew found the clavicle and the mining pit where Berger found its owner. Climbing down into the pit, he points onlookers to bits of fossils peeking out of the rock. The awestruck guests crane to glimpse an infant's arm bone and the lower jaw of a false saber-toothed cat. Just by gathering remains exposed by the miners and the occasional rainstorm, the team has amassed one of the largest fossil hominin samples on record. Once the researchers begin excavating the roughly 500-square-meter site, Berger knows they will find more bones—many more. Extensive planning is under way to erect a structure to protect the site from the elements and serve as a state-of-the-art field laboratory. Meanwhile, in the Malapa block lab at the University of the Witwatersrand, chunks of rock blasted from the miners' pit fill floor-to-ceiling shelves. Researchers are peering into the rocks with a CT scanner to look for more hominin bones, including the adult female's missing skull.

So vast are Malapa's riches that Berger could probably spend the rest of his career working on them. Yet already he is thinking about where he wants to go next. A. sediba “has taught me that we really need a better record—and it's out there,” he warrants. The mapping project that led Berger to Malapa identified more than three dozen new sites in the Cradle alone that could potentially harbor hominin remains. He is lining up researchers to dig the most promising of those spots. Berger himself has his sights set farther afield. The Congo and Angola have caves similar to the ones in the Cradle and have never been searched for hominin fossils, he observes. Perhaps there he will find another unexpected emissary from the dawn of humankind that will rewrite the story of our origins once again.