Genetics Steps In to Help Tell the Story of Human Origins
Genetics Steps In to Help Tell the Story of Human Origins

Genetics Steps In to Help Tell the Story of Human Origins

Africa’s sparse fossil record alone cannot reveal our species’ evolutionary history.

Katarina Zimmer
Katarina Zimmer
Sep 1, 2020

ABOVE: MODIFIED FROM © MARK GARLICK, SCIENCE PHOTO LIBRARY

It’s not unusual for geochronologist Rainer Grün to bring human bones back with him when he returns home to Australia from excursions in Europe or Asia. Jawbones from extinct hominins in Indonesia, Neanderthal teeth from Israel, and ancient human finger bones unearthed in Saudi Arabia have all at one point spent time in his lab at Australian National University before being returned home. Grün specializes in developing methods to discern the age of such specimens. In 2016, he carried with him a particularly precious piece of cargo: a tiny sliver of fossilized bone covered in bubble wrap inside a box. 

The bone fragment had come from a skull—still stored at the Natural History Museum in London—with a heavy brow ridge and a large face. It looked so primitive that the miner who had discovered it in 1921 at a lead mine in the Zambian town of Kabwe, then in the British territory of Rhodesia, first thought it had belonged to a gorilla. But later that year, museum paleontologist Arthur Smith Woodward noticed what he interpreted as typically human features, such as the skull’s thin and relatively large braincase, that motivated him to designate the specimen as its own hominin species. 

In the 1980s, however, museum paleoanthropologist Chris Stringer took another look at the skull and classified it as belonging to the species Homo heidelbergensis, an ancient hominin thought to be a human ancestor. Based on its primitiveness, Stringer says, most researchers guessed it was an early individual who lived around half a million years ago, some 200,000 years before the earliest Homo sapiens were starting to emerge. But nobody knew exactly how old the skull was. For decades, no dating method existed that could identify the fossil’s age without the destructive process of grinding up bits of bone for analysis. But Grün was determined to find a solution.

With few sediments, let alone fossils, left behind from that time, the birth of our genus is one of the most poorly understood periods in our evolution.

Grün is one of very few geochronologists proficient in a laser technique that extracts and reduces a barely visible grain of bone—smaller than the bone’s natural pores—to atoms, he says. The laser is coupled with a mass spectrometer, which measures the concentrations of uranium isotopes that undergo radioactive decay at a specific rate over time. 

Having returned from his trip to procure the Homo heidelbergensis sample, Grün watched as the laser poked two tiny holes into the bone fragment and the particles disappeared into the mass spectrometer. Upon evaluating the mass spec data, he could tell that the fragment was much younger than previously believed. As he, Stringer, and others reported in Nature this past April, their best estimate was 299,000 years, give or take 25,000. That meant that the Kabwe individual had lived not before, but around the same time as the first Homo sapiens–like people dwelled in North Africa. Along with other archaeological evidence, the findings suggest that perhaps Homo heidelbergensis was not our ancestor, but a neighbor. 

Together with yet another hominin, Homo naledi, known to have existed in southern Africa at that time, Africa may have been a crowded place. “Ten years ago, I think most of us would’ve thought, well, Africa in the last 300,000 years is just going to show you the evolution of Homo sapiens, and that’s really all—the other species would have disappeared, gone extinct,” notes Stringer. “Now we know that there were probably at least three different kinds of hominins around.” That’s akin to the situation that unfolded in Eurasia, where Neanderthals and Denisovans thrived for hundreds of thousands of years before Homo sapiens migrated out of Africa and at times even interbred with the other hominin groups. 

The story in Africa remains murky, however, as researchers have not been able to reconstruct human history in vivid detail, in part because hominin fossils informative about our species’ emergence and coexistence with other species are rare in Africa. As a result, finds such as the Kabwe skull continue to raise more questions than answers. If Homo heidelbergensis wasn’t one of our recent ancestors, then who was? If our species really did overlap in time with Homo heidelbergensis, what role did they play in our evolutionary history?  

In recent years, a field that has traditionally relied on fossil discoveries has acquired helpful new tools: genomics and ancient DNA techniques. Armed with this combination of approaches, researchers have begun to excavate our species’ early evolution, hinting at a far more complex past than was previously appreciated—one rich in diversity, migration, and possibly even interbreeding with other hominin species in Africa. 

“To piece together that story, we need information from multiple different fields of study,” remarks Eleanor Scerri, an archaeologist at the Max Planck Institute for the Science of Human History in Jena, Germany. “No single one is really going to have all the answers—not genetics, not archaeology, not the fossils, because all of these areas have challenges and limitations.” 

A sparse fossil record 

Bones easily disintegrate in many parts of Africa, in acidic forest soils or dry, sun-exposed areas. Moreover, the continent is largely unexplored by archaeologists. While northwestern Africa and former British territories in eastern and southern Africa have a long tradition of professional archaeological research, few researchers have looked for fossils anywhere else, notes archaeologist Khady Niang of Cheikh Anta Diop University in Senegal. That’s especially the case for the western and central parts of the continent, where preservation conditions are also poor and excavations difficult at times due to political instability. “We might be missing some really, really important parts of the story,” adds Yale University anthropologist Jessica Thompson. 

What African hominin fossils do make clear is the depth of humanity’s roots on that continent. Researchers have found some of the most abundant fossils in sediments between 3.5 million and 3.2 million years old. That appeared to be the heyday of the australopiths (including the genus Australopithecus), apes that walked upright and are believed to have used stone tools, but still climbed trees and had relatively small brains. It’s thought that somehow our own genus, Homo, emerged from transitional ape species some 2.8 million years ago as a clan of hominins with distinctive teeth, probably adapted to an eclectic diet that allowed them to thrive in a wide range of habitats. But there are few sediments, let alone fossils, left behind from that time, making the birth of our genus one of the most poorly understood periods in our evolution, Thompson notes. 

The fossil record yields more secrets about the time shortly after the emergence of Homo, revealing a diversity of different Homo species in Africa, of which Homo erectus seems to persist the longest. Homo erectus crops up in Africa’s limited fossil record around 2 million years ago and hangs around on the continent until roughly a million years ago. It was the first hominin that shows evidence of having lived in human-like social groupings and used fire, and it is thought to be a human ancestor. When and how Homo sapiens emerged isn’t at all clear, but what is apparent is that we weren’t alone; fossils suggest that several other hominin species, such as that represented by the Kabwe skull, inhabited the continent at the time our species appeared. Another relatively small-brained hominin, Homo naledi, is also thought to have lived in southern Africa around 300,000 years ago. And inside a Moroccan cave called Jebel Irhoud, 300,000-year-old skeletons were found that carry very early features of Homo sapiens. It’s not yet known how long those different hominin species existed, however, or whether they physically overlapped and perhaps even shared genes with one another, Stringer notes, or whether there were others. 

It was not a streamlined process of australopiths steadily evolving into modern humans, but a messy and haphazard journey that includes interwoven ancestries of many groups.

By around 160,000 years ago, the constellation of physical features that defines us today—such as a globular braincase and a pointed chin—had begun to emerge in ancient hominin groups represented by fossils found across Africa. Later, some of these anatomically modern humans crossed the thin spit of land that connects Africa to Eurasia, probably on several occasions. On that new continent, they eventually met Neanderthals and Denisovans, which, like two hobbit-size Homo species found on southeast Asian islands, are thought to be the evolutionary products of earlier hominin migrations out of the continent. “Africa was this sort of leaky faucet, and hominins were just dribbling out of it all the time,” Thompson says. 

Fossil finds over the years have steadily bolstered a long-held idea that anatomically modern humans first emerged in Africa. This “Out of Africa” model, proposed by anthropologists in the late 20th century, posited that all humans of Eurasian ancestry descended from a single ancestral African population, which then spread throughout the world and displaced all other hominins. The opposing “multi-regionalism” model, by contrast, conceived that multiple human subpopulations—which stemmed from regional lineages of an ancestral species such as Homo erectus—existed across Europe, Asia, and Africa, and through continuous mixing evolved together to form the present human population.   

While fossils supported the former theory, it was the advent of genetic research that showed unequivocally that populations outside of Africa descended from a single population in Africa. But the story had a twist: in two groundbreaking studies published in 2014, researchers compared ancient DNA extracted from Neanderthal bones and compared it with modern-day people, and found that 2 percent of the average European genome is Neanderthal in origin. Our species originated in Africa, but interbred with hominins outside of it. 

See “Neanderthal DNA in Modern Human Genomes Is Not Silent

These findings, and many since, have highlighted the power of genetics in resolving questions about human ancestry that fossils alone cannot. Investigations of the genomes of living Africans are now underway to help fill in the gaps of Africa’s fossil record. “[Such studies] are really providing important insights into our population history and African origins,” says Yale University evolutionary biologist Serena Tucci. “We are getting to know and understand processes that happened very early on in our evolutionary history.” 

Our History in Africa

Hominin fossils that reveal clues to the emergence of Homo sapiens are rare in Africa, but in combination with studies of modern human genomes, researchers are piecing together an ever more complex timeline of human history.

© MODIFIED FROM ISTOCK.COM, GIORGIOMORARA
See full infographic: WEB | PDF

Ghost hominins

Even the very first investigations of our genetic ancestry, gleaned from small, bite-size chunks of genetic material, positioned Africa as the cradle of humanity. One widely publicized 1987 study compared mitochondrial gene snippets from 147 people across the world, and concluded that Africans have the highest mitochondrial diversity, suggesting that our species originated and spent most of its evolutionary history there. Specifically, the authors traced all human mitochondrial diversity back to a single theoretical woman who lived in East Africa hundreds of thousands of years ago, whom the media popularized as “mitochondrial Eve.” Later studies estimated that the most recent common ancestor of modern Y chromosome variation (dubbed “Y chromosome Adam”) could also be traced back to Africa.  

Subsequent studies of nuclear DNA have validated our African birthplace and refined our knowledge of the human genetic landscape. Several studies of genetic variation among modern-day Khoe and San individuals, two groups of indigenous people in southern Africa known for their click language, have suggested they represent our species’ most genetically diverse lineage. Collectively known as Khoe-San, this group is thought to have split from other populations between 200,000 and 350,000 years ago, making them the most ancient population of modern humans to diverge. Non-Africans, meanwhile, represent a reduced subset of the diversity in Africa, and likely trace most of their ancestry back to just one small population—probably no more than a few thousand individuals—who ventured out of the continent between 60,000 and 70,000 years ago.

Some scientists see the extraordinary diversity in modern Khoe-San people as evidence that our species arose in southern Africa. Along with some archaeological evidence from the region, that challenges the long-held idea of an East African origin, which was based on the fact that many early hominin fossils were found there. However, trying to pinpoint the precise location of our species’ origins from DNA is often criticized for the simple reason that people move around—it’s not known if the populations living in one place today were there hundreds or thousands of millennia ago. In fact, some researchers, including Scerri, Stringer, and Thompson, have recently constructed an entirely new theory of our origins: that anatomically modern humans didn’t arise from a single place, but gradually emerged from a web of interconnected populations sprawled across Africa—a continental gene-sharing bonanza that hominin lineages besides our own may have participated in. “It’s a good way to interpret the data we have right now,” says Niang.  

In addition to where we evolved, researchers are interested in how: which genes gave us a selective advantage to survive in particular environments, and which ancestors contributed to our genomes? Unfortunately, modern African DNA is severely underrepresented in genetic research, making these questions particularly challenging to answer. Most sequenced genomes are of European origin, with fewer than 2 percent coming from Africans. This dearth of African genomes is compounded by the fact that the genetic scaffold underlying some frequently studied traits such as skin pigmentation appear to be far more complex in Africans than in other populations, notes Brenna Henn, a population geneticist at the University of California, Davis. “The twelve to fifteen genes [for skin pigmentation] that people cite in Eurasian populations explain less than 25 percent of the variation in Africans.”

African population history complicates matters further. Large-scale migrations pulled people back and forth across the continent for thousands of years. People from Eurasia also migrated back to Africa. Where people moved, they swapped their genes with local populations, shuffling patterns of ancestry across African genomes. This upheaval of ancient population structures creates one of the biggest challenges in teasing out archaic history from modern genomes, notes University of Pennsylvania geneticist Sarah Tishkoff. “It can make it very tricky to distinguish that older history when there’s been this newer wave of gene flow messing with your modeling.” 

Still, geneticists have been able to tease out some signals from our distant past, using computational models that ask what kind of evolutionary processes—such as mutation, selection, and interbreeding with other groups—best explain the pattern of variation across modern genomes. One intriguing finding of such studies is possible evidence of mixture with now-extinct, unknown groups of modern humans and other hominins: “ghost” populations that, like Neanderthals, left traces in modern genomes. In one analysis of 15 sequenced genomes, Tishkoff’s group investigated the sources of genetic variation in three different modern African hunter-gatherer groups. The team’s models suggested that interbreeding with an archaic hominin species—which seemed as different from modern humans as are Neanderthals—was the most likely origin for a set of unusual sequences they found. “The model that includes a ghost population is always better [to fit the data], basically,” Tishkoff says. 

A handful of similar studies have also revealed traces of ghost hominins in modern African genomes, sometimes accounting for up to 10 to 20 percent of the genetic variation. Some research suggests that mixing took place after the ancestors of modern Eurasians left Africa, hinting that other kinds of hominins could have existed alongside Homo sapiens in Africa until very recently. “It’s actually pretty convincing,” says Henn, who wasn’t involved in these studies. “Ten percent of the genome—I’m going to have a hard time invoking one single other process that can explain a signal like that.” 

Ultimately, researchers need samples of DNA from ancient hominins to prove whether archaic African species did in fact contribute to modern genetic variation. While scientists have managed to overcome some of the technical hurdles of sequencing highly degraded ancient DNA from human fossils in Africa, the oldest human DNA found on the continent is just 15,000 years old, an age that pales in comparison to some 400,000-year-old hominin DNA found in a cave in Spain with relatively cool, stable temperatures. Archaeologists can only dream of finding intact DNA that old on the African continent, notes Tessa Campbell, an ancient DNA specialist at Iziko Museums of South Africa. “No one wants to say never . . . but it’s very unlikely.” 

Because DNA is unlikely to survive very long in the African heat, researchers have largely refrained from drilling into the fossils they’ve found of other hominins in Africa for fear of destroying them. But efforts are underway to study ancient DNA from younger fossils of Homo sapiens to crack other mysteries about human history on the continent, Tucci notes. “This is definitely a new era for African genomics.” 

Excavating a Continent  

A number of researchers suspect that Homo sapiens arose not in a single place in Africa, but across the entire continent, emerging from a network of interconnected hominin populations. But for decades, archaeologists positioned East and South Africa as important places for hominin evolution and the putative birthplace of our species. That’s likely because most fossils, including groundbreaking findings that have transformed our understanding of human evolution, have been found in those regions.

WIKIMEDIA, 120; ARIZONA STATE UNIVERSITY; WIKIMEDIA, BAHN, PAUL G; WIKIMEDIA, GERBIL; WIKIMEDIA, RYAN SOMMA; ELIFE, 6:E24232, 2017; WIKIMEDIA, GUILLAUMEG

KABWE, ZAMBIA, 1921 

“Kabwe skull,” 300,000 years ago

Also called “Broken Hill skull,” the specimen is considered a representative of Homo heidelbergensis.

NEAR SAFI, MOROCCO, 1961 

Human remains at Jebel Irhoud, 315,000 years ago

Flint blades and Homo sapiens–like skeletons in a Moroccan cave known as Jebel Irhoud may represent the oldest Homo sapiens artifacts. The skeletons have modern features such as round skulls and modern-human–like teeth and faces.

OMO NATIONAL PARK, ETHIOPIA, 1967-1974 

Omo Kibish remains, 195,000 years ago

Fragments from two skulls, four jaws, a legbone, a few hundred teeth, and some other bones were found at a site in Ethiopia, and are classified as anatomically modern Homo sapiens.

AFAR REGION, ETHIOPIA, 1974

“Lucy,” 3.2 million years ago

Lucy—the skeletal remains of an Australopithecus  afarensis female—is one of the best-known hominin fossils. Studies suggest that she was both tree-dwelling and capable of an upright gait, providing an important evolutionary stepping stone from more primitive ape species to modern humans.

LAKE TURKANA, KENYA, 1984

“Turkana Boy,” 2 million years ago

A nearly complete skeleton of an ancient Homo erectus child found near Kenya’s Lake Turkana provides a rare glimpse into how quickly this species reached adulthood and how similar their skeletons were to ours.

RISING STAR CAVE, SOUTH AFRICA, 2013

Homo naledi, 236,000–335,000 years ago

In 2013 and 2014, cavers found skeletons of two adults and one juvenile of what is believed to be a new species: Homo naledi. Its tiny brain and ape-like shoulders—indicating it was a good climber—suggest it may be an evolutionary off-shoot lineage that went extinct.

AFAR REGION, ETHIOPIA, 2013

Adult jawbone, 2.8 million years ago

A mandible fragment is the earliest known trace of the genus Homo, although the species it belongs to is a mystery. 

See full infographic: WEB | PDF

Mining bones for ancient DNA  

In 2015, an international team of researchers managed to harvest the first ancient DNA in Africa—the genome of Mota, a man who left behind 4,500-year-old remains in an Ethiopian cave. In the five years since that publication, researchers have published nearly 100 other full and partial ancient human sequences from Africa. These genomes have helped scientists better understand the messy signatures from recent migration events that make studies of modern genomes so difficult. 

For instance, mitochondrial DNA from the skulls of seven people who lived some 15,000 years ago in modern-day Morocco revealed that they were closely related to Natufians, hunter-gatherers who dwelled in the Near East, as well as people living south of the Sahara desert. This finding suggested that there were far-flung connections between North Africa, the Near East, and sub-Saharan Africa  before the dawn of agriculture. 

Analyses of ancient DNA have also helped researchers understand how ancient migrations affected the genomes of people alive today. One such migration is the Bantu expansion, which gradually spread West African farming practices across the continent between roughly 5,000 and 1,000 years ago. By comparing DNA from ancient hunter-gatherer remains in southern Africa with modern-day Khoe-San people, evolutionary biologist Carina Schlebusch of Uppsala University in Sweden and her colleagues found that some Khoe-San groups carry DNA that ancient farmers brought with them. They also carry mixed Eurasian ancestry that had been introduced to North Africa with earlier back-migrations into the continent and eventually carried to the southernmost tip of Africa as other migrating human populations moved southward, the researchers found. 

Such studies have also provided insight into deep divergences that occurred in human populations long before migrations of farmers and herders. Mary Prendergast, an anthropologist at Saint Louis University in Madrid, and her colleagues recently sequenced the first ancient DNA from West Africa, material extracted from the remains of children buried inside a rock shelter in Cameroon. Comparing the 3,000- and 8,000-year-old DNA with ancient genomes collected elsewhere and with genomes of modern people allowed the researchers to reconstruct some of the earliest branches of our species’ evolutionary tree. In addition to the deep split between Khoe-San groups and other African populations—from which non-Africans also descend—their model suggested that two other major lineages split just as deeply, diverging from one another more than 200,000 years ago. One lineage is ancestral to central African hunter-gatherers known as Aka and Mbuti, and the second is a previously unknown “ghost” lineage whose fate is uncertain. “There’s all this deep, deep population structure with various differentiated branches of the human tree throughout the Pleistocene in Africa that we haven’t really appreciated very much yet,” Prendergast says. 

Only time will tell whether researchers’ current arsenal of technologies is enough to untangle the complete story of human evolution. Perhaps novel technologies—such as paleoproteomics, a nascent field that aims to reconstruct ancestry from fossilized proteins, which are more durable than DNA—will help researchers “push further back in time,” notes biological anthropologist Rebecca Ackermann of the University of Cape Town.  

What is already abundantly clear is that human evolution was far more complex than previously appreciated by anthropologists. It was not a streamlined process of australopiths steadily evolving into modern humans, but a messy and haphazard journey that includes interwoven ancestries of many groups, some of which have never been discovered other than through the genetic traces they left in ancient and modern genomes. “We have a long history. A lot of things happened, and a lot of ancestors contributed to our genomes today,” Schlebusch says. “It’s not going to be a simple story.” 

Decolonizing Studies of Human Evolution

The San people of southern Africa are one of the most intensively studied indigenous groups in the world. Their click language and traditional hunter-gatherer lifestyles have long fascinated anthropologists. And the antiquity of their genetic lineage makes them a treasure trove for geneticists studying human evolutionary history. 

However, studies on San lifestyles and genomes have not always been conducted ethically. For instance, scientists have sometimes referred to the San as “bushmen,” a derogatory term associated with colonial-era researchers using modern indigenous groups as models of primitive human ancestors, and have taken photographs of children and breastfeeding mothers without permission. “We’re not saying that everybody is bad. But you get those few individuals who don’t respect the San,” Leana Snyders, head of the South African San Council in Upington, South Africa, told Science in 2017. Ethical conduct in genomic research came to the foreground in 2010 following a high-profile analysis of San genomes in Nature in which the authors had, among other transgressions, not asked San leaders for permission to conduct the study.  

All disciplines that study human evolution in Africa have at times been criticized for their extractive nature. Archaeological research—a field pioneered by European colonial nations—has long been driven by Western researchers digging up fossils from Africa to study them, sometimes taking them elsewhere to do so. Some hominin fossils are still displaced, such as the Kabwe skull, a famous Homo heidelbergensis specimen that remains in London’s Museum of Natural History, despite Zambia’s multiple requests to repatriate the skull. According to an April press release, the museum has approached Zambian authorities to begin discussing the possible return of the skull following a 2018 agreement between the UK and Zambia to find a solution to the issue. 

Some scientists have called for regulations to protect fossil collections from ancient DNA research, whereby African hominin fossils undergo the damaging process of extracting DNA. Now, “African museums are taking a leading role to make sure this [research] happens through collaboration and regulation,” notes anthropologist Mary Prendergast of Saint Louis University’s Madrid campus, as geneticists are working to develop new, less destructive techniques for ancient DNA analysis. 

The San, for their part, created a code of research conduct in 2017 that, for example, requires researchers to respect their communities and to allow them to comment on findings prior to publication to avoid derogatory interpretations. Researchers are also required to compensate the community for their cooperation, through financial support, knowledge, or job opportunities, for instance.

A number of scientists have called for a greater role of African scientists in human evolutionary research. To make that possible, Western funding agencies and institutions have an obligation to support African efforts to improve their countries’ antiquities infrastructure, so that “the next generation of African scholars [can] take control of the research in their areas,” notes anthropologist Eleanor Scerri of the Max Planck Institute in Germany.

Foreign research teams should also foster stronger collaboration with African researchers, rather than simply seeking their help with fossil excavations, which has sometimes been the case, notes University of Cape Town biological anthropologist Rebecca Ackermann. Research groups have become more diverse, she notes, but the transition is slow. “I do see a change. It’s just not as fast as I would like.”