Moving deftly through the semi-lit cave in northern Croatia, a team of paleontologists is on the brink of discovering a secret that has remained forgotten for thousands of years. At their feet lie tangled and fragmented bones embedded within the cave floor, their dilapidated, disorganized appearance concealing the valuable microscopic clues hidden inside. Even after their discovery, many of these broken pieces of bone from the Vindija cave are declared unidentifiable, put aside for years, and forgotten once more.

Twenty years later, Dr. Tim White, a world-renowned paleoanthropologist from UC Berkeley, reexamined the collection in Croatia and noticed the remnants of an ancient hominid (a close relative of the human species) lying among the skeletal remains of cave bears and other large mammals. This hominid had evolved and lived alongside early modern humans. White’s identification of these bones as Neanderthal fossils proved to be serendipitous when the Croatian curator of the collection brought the discovery to the attention of a distinguished expert on ancient DNA.

The bone fragments that emerged from the darkness of that cave, thousands of years after living Neanderthals entered it for the last time, soon embarked on a journey to Leipzig, Germany, home to leading scientists in the field of evolutionary anthropology. There, DNA sequences from these bones were used to construct a complete genome of the Neanderthal. Then, once again the sample—this time in the form of an ancient genome—traveled around the world and back into the hands of UC Berkeley biologists.

The study of human evolution requires multiple scientific disciplines to piece together clues left behind by our ancestors—their bones, artifacts from their environment, and, if we’re lucky, their enigmatic genomes. UC Berkeley scientists and their collaborators are putting these pieces together to help us delineate our unique evolutionary history. Together, these studies have revealed some surprising truths. Indeed, our very ability to adapt to new environments as we canvassed the globe may have been influenced by ancient interactions with our hominid relatives.

A twig on the evolutionary tree

To visualize how evolution gave rise to millions of species, imagine an enormous and intricate tree with millions of branches of different shapes and sizes. Each branch represents a unique species, and the length of the branch represents how long the species has existed on Earth. Trace backwards to the joint of each branch to find the last common ancestor, an extinct species that gave birth to others that lived on, some splitting into more and more branches.

Individuals of a species can spontaneously gain mutations, and in new environments, natural selection begins to shape evolution. Individuals with beneficial mutations, which provide an advantage in survival and reproduction, fare better in the new environment and pass on those new genes to their offspring. Eventually, beneficial genes become more common in the population, and at some point these genetic changes accumulate to the point that individuals can no longer reproduce with the original population—marking the birth of a new species.

Although we follow the same evolutionary “rules” as every other species on Earth, modern humans are strange in comparison.

“Humans are outliers in terms of our range, our behavioral flexibility, our intelligence, and our culture,” White says. Besides our unique traits, we are also prolific: there are seven billion of us, and no other animal has influenced the planet as significantly as we have. Humans have changed the biological landscape to such a degree that geologists have proposed to name the current geological period Anthropocene after our species.

Since our ancestors departed from their home in Africa, we have dramatically expanded our geographic range. As we adapted to new environments, our DNA evolved with us. Today, our evolutionary history is written within our DNA code. Can we accurately trace the steps of our ancestors to figure out how modern humans came to be? And will understanding our evolutionary past help explain our present and prepare us for the future?

Unearthing ancient bones and final resting places

Bones are the longest-lasting relics of our ancestors, and finding them preserved with fragments of their ecological landscape is the first step toward investigating our past. Fossilized bones can remain embedded in cold cave floors or stratified sediments for up to millions of years, but even these well-preserved bones can be difficult to find.

“Hominids are very rare,” White says. “Not only are they few and far between on any landscape, but [they] live for a long time…The number of dead individuals per hundred years is a lot smaller than, for example, mice or bears.” Reconstructing the path of human evolution requires teamwork from scientists around the world, as exemplified by White’s international collaboration that resulted in the Neanderthal DNA discovery.

The Human Evolution Research Center (HERC) at UC Berkeley is home to scientists working to uncover the history of our species, and today HERC serves as a nexus for paleontology, anthropology, geology, and more recently, molecular biology.

“You have to bring in those different dimensions; there’s really no [other] option,” says White, who is currently a professor of integrative biology and director of HERC. “Berkeley has done that very well for a very long time.”

Human evolutionary research at UC Berkeley began in the early 1900s and was transformed in 1970 when celebrated anthropologist F. Clark Howell founded the Laboratory for Human Evolutionary Studies. Since its inception, the program has made teaching and public outreach top priorities, while concurrently generating skilled, well-rounded paleoanthropologists.

HERC, which grew out of the Laboratory for Human Evolution Studies, sends many UC Berkeley students to Africa—the birthplace of our species and the continent with the longest record of human evolution—as part of their undergraduate and graduate training. In particular, students journey to the Middle Awash, a significant paleoanthropological site resting along the Awash River in Afar, Ethiopia. Some of the earliest known hominids were discovered in the Middle Awash, and the site has accommodated UC Berkeley scientists off and on since the 1980s.

Middle Awash team members working to reconstruct the skeleton of a Pleistocene lion from the Middle Awash study area, Ethiopia, in the Paleoanthropology Laboratory at the National Museum in Addis Ababa. Credit: Tim White.

HERC has been involved in the excavation and study of thousands of vertebrate fossils, including those from multiple hominid species that can be traced back through our lineage. Their work includes the discovery and analysis of several members of the Ardipithecus and Australopithecus genera, some of the oldest known hominids. UC Berkeley scientists also uncovered many skeletons of our own genus, Homo, including Homo habilis, Homo erectus, and early Homo sapiens. Paleoanthropologists, like HERC graduate student Josh Carlson, depend heavily on the discovery of new specimens for honing their understanding of human evolution. “You test hypotheses with evidence, and new fossil evidence is generated through fieldwork,” he says.

When the fossilized remains of a hominid are found, scientists treat the site of an excavation like a forensic crime scene. The bones, the sediments in which they lie, and any other nearby fossils are used to reconstruct the habitat of the ancient hominid. The discovery of the bones belonging to the species known as Ardipithecus ramidus, found in sediments along the Awash River in the 1990s, required White and his graduate students to take great care in their excavation and analysis.

Indeed, several graduate students were responsible for many of those essential findings, including the discovery of “Ardi,” the oldest and most complete hominid skeleton ever found. This female hominid lived about 4.4 million years ago and pre-dates Australopithecus afarensis (“Lucy”) by 1.2 million years. In addition to the bones of other Ardipithecus individuals, the fossils of other mammals, invertebrates, and botanicals from the same geological time period have also been collected, providing an ecological context for the hominid bones.

“Hominids are one target of fieldwork, but we’re interested in the entire community or ecosystem,” says Carlson. A full description of Ardi—what she looked like, how she moved and behaved, and what kind of environment she lived in—required 15 years of careful excavation, extraction, and detailed analysis by an international team of paleontologists to complete.

Ardi’s skeletal fragments, which included the skull, teeth, pelvis, hands, and feet, revealed that Ardipithecus ramidus had a mixture of ape-like and human-like characteristics. Ardi was similar to chimpanzees in her stature and brain size, but she had small canine teeth, a short cranium, and a small face—unique hominid traits.

“[The emergence of] bipedality, and the loss of the canine honing complex [which allows the lower teeth to sharpen the upper canines], appear to have been among the first things that happened after we parted evolutionary company with the chimpanzees,” says Carlson. Evidence suggests that while Ardi spent some of her time in the trees, moving along branches using all four limbs, she also walked upright on the ground as a biped. By examining the shape and isotopic composition of Ardi’s tooth enamel, alongside thousands of neighboring fossils, paleontologists surmised that this population of hominids lived in a woodland area and had an omnivorous diet, likely based on nuts, fruits, insects, and small animals. This interpretation of Ardi’s features and habitat differs from the long-held belief that living in the open savannah led to the development of bipedalism, and it also shows that the last common ancestors of humans and apes were distinct from currently-existing apes, which have been evolving along their own lineages for millions of years.

Because the fossils of ancient animals do not have any organic material left on which to perform traditional carbon dating, researchers determine the age of ancient hominids like Ardi by analyzing volcanic rock and ash found interbedded with hominid remains. The Berkeley Geochronology Center, established by UC Berkeley geologist Garniss Curtis and currently directed by Earth and Planetary Science Professor Paul Renne, works closely with paleontologists to date various volcanic samples. In the 1960s, UC Berkeley scientists first used potassium-argon dating, a method developed by a UC Berkeley physicist, to date volcanic deposits found with a fossilized hominid from Tanzania. That collaboration marked the first of many between paleontology and geochronology throughout the world. Analyzing the unique geochemical fingerprint of ash, which is associated with specific volcanic events, helps researchers correlate geological events with nearby skeletal remains, effectively dating the specimen. For example, Ardi was found between two volcanic ash layers that were both dated to 4.4 million years old, which provided Ardi’s age with remarkable resolution. “We are blessed with these accidents of geology,” White says.

Salvaging ancient DNA from fossilized bones

The architecture of our ancestors’ bones can show us how the human lineage physically changed over time, but the story of our evolution is also written in our DNA. Innovations in biotechnology have made it possible to extract and sequence miniscule quantities of ancient DNA from well-preserved hominid bones. The Neanderthal bones taken from the Vindija cave and later scrutinized by Tim White eventually made their way to the Max Planck Institute in Germany. In the safety of a clean room, their microscopic secrets were extracted and sequenced, generating the Neanderthal genome in 2010.

Genomic data makes it possible to identify and distinguish among independent hominid species, even when little fossil material is available. In 2010, scientists found a finger bone from a possible hominid in the Denisova cave in Serbia. Even without additional skeletal pieces, the fragment of bone was dated, and its DNA was extracted. The resulting genome proved that the finger bone did not belong to Neanderthals or early modern humans, but rather to Denisovans, another distantly-related hominid that lived during the same time period.

After the DNA sequence of a hominid fossil is obtained, specialists in population genetics, like UC Berkeley’s Montgomery Slatkin, professor of integrative biology, are brought in to make sense of the information. Slatkin, whose background is in mathematics, works with his laboratory to analyze ancient hominid and modern human genomes, looking for patterns hiding in the DNA. The Slatkin lab then scrutinizes various scenarios that could explain these patterns, such as human migration or cross-hominid reproduction. “I always describe this as trying to put together a piece of furniture from IKEA,” Slatkin says. “You have to make everything fit, and you have to have no pieces left over.” The approach has been quite fruitful. Using statistical tests for each possible scenario, the Slatkin lab and their collaborators recently discovered an unexpected chapter of our evolutionary story.

By analyzing DNA from Neanderthals, Denisovans, and Homo sapiens, Slatkin and his colleagues found that these three groups of hominids interacted with and even reproduced with one another—examples of “admixture,” or the interbreeding of related species. Today, all modern humans outside of Africa carry small remnants (about 2 percent) of Neanderthal DNA as a result of these unions, which occurred only 70,000 years ago. Denisovans reproduced with the ancestors of modern day humans from the Oceania region, and to this day, people from Papua New Guinea, Australia, and a few islands of Southeast Asia still carry about 4-5% of this genetic signature with them. The Denisovan genome also revealed admixture with yet another unidentified ancient hominid sometime in its past; some speculate that this mystery hominid was Homo erectus. “Certainly the surprise was how many human relatives there have been, and how much interbreeding among them there has been,” Slatkin says.

Australopithecus skulls and jawbones, found in Ethiopia, are among the fossils in HERC’s collection. Credit: HERC.

In an interesting twist, human genomes today bear no evidence of Neanderthal or Denisovan mitochondrial DNA, which can only be maternally inherited. Similarly, there is also no evidence of paternally inherited Neanderthal or Denisovan Y chromosomes. While this may be due to the low rate of interbreeding between these groups, other evidence points to genomic incompatibility. Certain genetic sites don’t show evidence of transfer from Neanderthal and Denisovan genomes into our own, suggesting that there might have been a minor reproductive incompatibility between Neanderthals, Denisovans, and our ancestors.

To this day, the extinction of Neanderthals and Denisovans remains a mystery. However, the fact that these hominids coexisted with humans points to another riddle—why were Homo sapiens the only hominids that survived from that time period?

“I actually think culture is the answer,” Slatkin says. “Life was hard for Neanderthals and Denisovans, and genetic analysis shows that those populations were small, and they were declining. I think modern humans had a more effective culture that allowed them to deal with these harsher conditions. [Perhaps] they were better at hunting, communication, [or] exploiting other natural resources.”

Today, Slatkin and his lab are screening the DNA of different Neanderthal individuals to understand how they evolved as a group. Slatkin himself optimistically awaits the possibility of extracting DNA from other hominid fossils, such as Homo erectus. Although the chances of finding well-preserved DNA from a Homo erectus fossil are not high (largely due to a hot African climate that speeds up DNA degradation), the information gained by sequencing fossilized genomes could transform our understanding of these hominids.

Using ancient DNA to understand human adaptation

The global expansion of the human species is impressive considering that we originated from a single continent. How did we adapt to new and strange habitats as we migrated throughout the world? The bones collected by the hands of paleontologists, like those from the Vindija and Denisova caves, continue to yield answers in unexpected ways, providing evidence of evolutionary adaptation in their DNA.

Rasmus Nielsen, professor of integrative biology at UC Berkeley, seeks to understand how prehistoric events defined our biology by searching for genetic traces of adaptation in old hominid genomes. As our ancestors traveled from their home, they encountered less-than-hospitable conditions: extreme changes in altitude or temperature, unfamiliar food sources, and new pathogens, to name a few. Only the fittest humans managed to survive in these new environments and pass their genes down to modern humans. Using various mathematical and computational methods, the Nielsen lab traces how our genomes have changed over evolutionary time.

Recently, the Nielsen lab analyzed the genetic changes that allow people to live in high altitudes. The Tibetan people live among the Himalayas, the highest mountain range on Earth, and are able to survive more than 4,000 meters above sea level. At this altitude, the amount of oxygen inhaled in a single breath of air is 40 percent lower than the oxygen found in a breath of air at sea level. Individuals unaccustomed to this environment would first experience shortness of breath and altitude sickness living at this elevation. Over time, however, prolonged exposure to such thin air could lead to cardiovascular problems, like high blood pressure, thanks to the body’s over-production of new red blood cells in response to the oxygen-depleted air.

Remarkably, the Tibetan people adapted to these harsh conditions due to changes at the genetic level. Nielsen and his students identified an altered version of a particular gene in Tibetans, called EPAS1, which is involved in regulating the body’s low oxygen stress response. This gene modifies the hemoglobin concentration in the blood and protects Tibetans from the negative health effects of living at high altitudes. Unexpectedly, this gene originated in the Denisovan hominids and was passed down to Tibetans through admixture.

Genomic evidence reveals that Neanderthals also contributed beneficial genes to modern humans. Neanderthals had been living outside of Africa for about 200,000 years before they began interacting and mating with ancient Homo sapiens. Researchers believe that Neanderthals possessed a more complex immune system than our early ancestors and that Homo sapiens inherited genetic elements of this improved immune system via admixture with Neanderthals—an unusually clear example of the evolutionary benefits of hominid interbreeding. Nielsen’s lab continues to hunt for further adaptations that our species may have gained through admixture with our hominid relatives.

In fact, some human populations carry genes that may have once helped their ancestors survive in harsher conditions, but are now detrimental in the context of our modern lifestyles, says Nielsen. One clear example of this shift in a gene’s utility can be found in the human diet. Certain populations, such as the Inuits, who live in cold climates, carry genes that helped their ancestors to survive with a diet low in sugar. These genes slow down the intake of sugar into cells. Today, these same genes predispose modern Inuits to diseases like type II diabetes.

Nielsen believes this type of information can help us make informed decisions about our health in the modern world. “We’re not eating the way that we have adapted to eat,” Nielsen says. “We can use genomics to inform us about diet.” Ultimately, studying our evolutionary past may provide us with guidance for the future.

Design: Jo Downes. Sahelanthropus: Didier Descouens. Ardipithecus: Tim White. Australopithecus: 1997. Habilis: lilyundfreya. Erectus and Neanderthal: Tim Evanson. Denisovan tooth: Thilo Parg. Click to enlarge.

The journey continues

A recent discovery—a collection of nearly 1,600 hominid bones found in South Africa—makes it clear that we’ve only unearthed a fraction of our ancestors’ surviving fossils. These fossils may represent an entirely new branch of the hominid family tree. Dubbed Homo naledi, this new hominid displays a mixture of characteristics evocative of both Australopithecus and Homo, and marks the beginning of another fruitful research endeavor.

While many questions about Homo naledi have yet to be answered, including its evolutionary position among our ancestors, the fossils represent another serendipitous peek into our evolutionary past. Their existence speaks to the unimaginable trove of knowledge we have yet to unearth about our evolutionary past. What did our ancestors look like? How did they live? How did they thrive and come to dominate our entire planet? Such questions have been at the tip of our imagination since the beginning of recorded history. As we continue searching for the answers, within caves, bones, and genomes, we will better understand our own strengths and weaknesses, our complex past, and our likely future.

This article is part of the Fall 2015 issue.