Lush Okavango Delta Pinpointed as Ancestral Homeland of All Living Humans

Genetic evidence traces our origins to a hunter-gatherer community that lived 200,000 years ago, but the study has generated controversy   

By Richard Conniff on October 28, 2019

Juǀ’hoansi hunters ǀkun ǀkunta, Nǂamce Sao and ǀkun Nǂamce re-creating how our ancestors hunted when the Homeland was once a vast wetland. ǀkun ǀkunta, Nǂamce Sao and ǀkun Nǂamce today live within the dried Homeland. Credit: Chris Bennett

Anyone lucky enough to have visited the Okavango Delta in the southern African nation of Botswana will recall the comforting and oddly familiar sensation of looking out from the shelter of a stand of trees at the panorama of wildlife—from elephants and African wild dogs to lilac-breasted rollers—moving across the lush surrounding floodplains. That sense of familiarity may run deeper than we imagine, a new study suggests—back to a time when early modern humans also wandered there.

The study, appearing Monday in the journal Nature, uses genetic, archaeological, linguistic and climatic evidence to argue that the ancestral homeland of everyone alive today was in northern Botswana—not in East Africa, as previously thought. Based on mitochondrial DNA, passed down from mother to daughter, the paper’s co-authors argue that we are all descended from a small community of Khoisan hunter-gatherers who lived 200,000 years ago in vast wetlands encompassing Botswana’s Okavango Delta and the Makgadikgadi regions.

Much of that place is now a dry salt pan—and inhabited by modern Khoisan people, sometimes called Bushmen. But back then, it was a vast wetland covering an area the size of Switzerland. The community that lived there was unusually stable, thriving almost unchanged for 70,000 years in a habitat closely resembling the modern Okavango Delta, according to senior author Vanessa M. Hayes, a geneticist at the Garvan Institute of Medical Research in Australia.

The new study looks at the mitogenomes, or mitochondrial genomes, of 1,217 individuals from multiple southern African ethnic identities, and focuses on a “rare deep-rooting” lineage called L0, or L zero. It’s the oldest known mitochondrial lineage, passed down intact from mother to daughter across the generations, though mutations can sometimes occur and may be associated with important evolutionary changes. Hayes became interested in that lineage as a result of her work with the South African Genome Project, which found evidence of L0 ancestry distributed across southern Africa. Archbishop Emeritus Desmond Tutu, descended mainly from Bantu groups who migrated into southern Africa 1,500 years ago, was among those identified as having Khoisan ancestry, a connection he said left him feeling “very privileged and blessed."

Tracking the accumulation of mutations in the L0 lineage across the eons provides geneticists with a time stamp for evolutionary changes. The co-authors of the Nature paper identify and date changes in the L0 lineage. They also correlate these “branching” events with evidence of climatic shifts, as well as with archaeological evidence of human migrations. During the initial 70,000 years of stable habitation, says co-author Axel Timmermann, a climate scientist at Pusan National University in South Korea, migration was probably constrained by harsh, dry conditions in the surrounding landscape. But about 130,000 years ago, a period of increased rainfall opened a green corridor for migrations to the northeast. Then, about 110,000 years ago, drying conditions within the homeland and opening of a green corridor to the southwest led to further migrations down to the southern tip of Africa. Evidence of both events survives, according to the study, in subgroups of the L0 lineage found in living descendants of those migrations.

The new research fits with other recent genetic evidence of human origin in southern Africa, including a study earlier this year suggesting that a migration from that region to East Africa, and the resulting mixture with populations there, might have been a key turning point in the evolution of modern humans and their migration out of Africa. Another paper this year also argues that a migration from southern Africa to East Africa immediately preceded a major out-of-Africa migration 100,000 to 70,000 years ago. The alternative pan-African, or “polycentric,” viewpoint holds that multiple interlinked populations evolved across the continent, sometimes in isolation and sometimes together.

James Cole, an archaeologist at the University of Brighton in England, who was not involved in the new study, praises Hayes and her colleagues for their cross-disciplinary approach to understanding mitochondrial evolution. But he also notes that their paper overlooks major archaeological evidence, such as the 315,000-year-old skeletal remains of an anatomically modern human recently found in Morocco. Hayes replies that her study focuses only on the population of direct ancestors of “people walking around today,” and in the absence of genetic evidence from the Morocco specimens, the connection to living humans is unknown.

Milford Wolpoff, a paleoanthropologist at the University of Michigan who also was not involved in the new work, similarly argues that the evidence its authors present is too narrow. Reliance solely on mitochondrial evidence leads to misinterpretation, he says, and risks overlooking important evolutionary information in the separate DNA of the cell nucleus. Our widespread inheritance of Neandertal genes shows up, for instance, only in the nuclear DNA, and it is completely absent from the mitogenome. Likewise, Wolpoff says, “the nuclear genome, with three billion base pairs, might tell an entirely different story about the African origin of modern humans from what the mitogenome’s 16,000 base pairs” suggest.

“We’re dealing with a puzzle of a million pieces,” Cole says, “and we’ve probably got the first 100 in place.” Paleogenetics has “ramped up the scale of complexity exponentially,” he adds. “From the paleontological and archeological record, it was a 1,000-piece puzzle.” But instead of providing a grand answer to the story of human origin, Cole suggests, so far, genetics is mainly showing us just how complex that story really is.

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Okavango Delta Pinpointed as Ancestral Homeland of All Living Humans

Author: Richard Conniff

Publication: Scientific American

Publisher: SCIENTIFIC AMERICAN, a Division of Springer Nature America, Inc.

Date: Oct 28, 2019

Copyright © 2019, Scientific American, Inc.

Mind Your “Fs” and “Vs”: Agriculture May Have Shaped Both Human Jaws and Language

Eating porridge and cheese appears to have changed our bite to enable the vocal tract to produce new sounds.

By Anne Pycha on March 14, 2019

Paleolithic flat bite (left) differs from a modern protruding bite (right). Credit: Tímea Bodogán

The organs of speech are the same for all people, or so linguists have typically assumed. But it turns out that may not be true—in fact, what you eat can change how you talk.

The conventional wisdom held in the field of historical linguistics is the vocal apparatus of human beings has remained fixed since the emergence of Homo sapiens some 200,000 years ago. As a consequence, all humans, both ancient and modern peoples, possess the same basic capacity to produce speech sounds. But recent evidence from several studies in paleoanthropology has upended these assumptions by suggesting the way we eat can actually alter jaw anatomy. And according to research just published in Science, the consequences for the way we speak have been profound.

The lead authors of the study, Damián Blasi and Steven Moran of the University of Zurich along with colleagues, became intrigued by fossil evidence showing the form of the human jaw had changed in our species’s relatively recent evolutionary past. Among hunter–gatherers of the Paleolithic period, adults’ upper and lower teeth aligned to form a flat line, the top ones resting directly on the bottom set. Scientists attribute that configuration primarily to tooth wear brought about by chewing hard foods, such as unmilled grains or seeds. With the advent of agriculture in the post-Neolithic period, however, the upper teeth protruded over and above the lower teeth, presumably due to the reduced challenge of consuming soft foods such as porridge and cheese.

These findings suggest not only that the cultural shift that gave rise to agriculture occasioned a shift in human anatomy. It also appears to have introduced new speech sounds known as labiodentals—the “f” and “v,” for instance. Blasi and Moran’s study furnishes evidence that adopting the signature foodstuffs of sedentary society ultimately allowed us to mouth words like “farro” and “verbalize” by raising the lower lip and bringing it into contact with the upper teeth. Their research group conducted biomechanical simulations of this movement using two different virtual jaws to calculate the muscular effort involved. Their results showed, compared with the protruding bites, the flat bite configurations required substantially more effort to produce a labiodental.

Linguists had already established that articulatory effort can affect the fate of a phoneme, so Blasi and Moran’s team speculated that labiodentals would have been less likely to emerge among any population with flat bites, such as Paleolithic humans, or even modern humans who eat harder foods. To test this hypothesis, they analyzed databases of the world’s consonants and showed contemporary hunter–gatherer languages contain only a fraction of the labiodental sounds that food-producer languages do. Of course, food preparation techniques are merely a stand-in for actual bite configurations. To make the link more explicit, the researchers separately analyzed hunter–gatherer societies in Greenland, southern Africa and Australia, where flat bites have been explicitly documented. In line with their hypothesis, results turned up relatively few languages with labiodentals among these populations. When one of these sounds appeared, it was usually borrowed from other languages.

As a final piece of support for their argument, Blasi and Moran’s team examined sound changes in Indo-European languages over time. They used a nontraditional technique called stochastic character mapping, which calculates the numerical probability a sound existed in a language at a particular point in time. Results showed labiodental sounds were extremely unlikely in almost all branches of Indo-European, until anytime from 6,000 to 4,000 years ago. After that period, which coincides with the introduction of soft foods, the probability of these sounds showed a notable increase.

The take-home message: “we can’t take for granted that spoken languages sound the same today as they did in the distant past,” Moran says. “This means in particular that the set of speech sounds we use has not necessarily remained stable since the emergence of our species, but rather the immense diversity of speech sounds that we find today is the product of a complex interplay of factors involving biological change and cultural evolution.”

Not everyone is convinced of the arguments put forth in the new study. Israel Hershkovitz of Tel Aviv University points out many factors besides tooth wear can affect bite configurations. Also, tooth wear occurs gradually and does not fully affect bite dynamics until adulthood. Given the relatively short life expectancy of prehistoric hunter–gatherers, he says, it seems unlikely this anatomical trait could have affected language evolution.

To other observers, Blasi and Moran’s study, along with others in recent years, reflects a paradigm shift in historical linguistics. “This paper revives an idea that linguists probably abandoned out of a natural apprehension—the danger of verging on ideas that could be interpreted as racist—which arises whenever anatomical differences between populations are proposed to play a role in any aspect of language or cognition,” says Andrew Garrett of the University of California, Berkeley, who was not involved in the study. “Today, however, there is clear evidence that individual anatomical, physiological and perceptual differences do play some role in linguistic differences.”

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Cave That Housed Neandertals and Denisovans Challenges View of Cultural Evolution

Researchers have deduced which early human species occupied Denisova Cave and when, drawing surprising conclusions about who made the sophisticated artifacts found there

By Kate Wong on January 30, 2019


Deep in the Altai mountains of southern Siberia sits a very choice piece of real estate. It’s nothing so newfangled as a ski lodge or one of the traditional wood houses that dot the local countryside. Rather it’s a primeval limestone cave, called Denisova, that overlooks a rushing river and the surrounding forest. Multiple human species, or hominins, have sought shelter in this cave over the past 300,000 years, such is its allure. Artifacts, bits of bone and ancient DNA found in its chambers testify to the presence of these peoples. The site thus offers a rare window on a particularly fascinating period of human evolution, one in which other human species coexisted with our own kind.

Researchers have long wondered how these groups interacted and influenced one another culturally when they met up, and Denisova could be a key to answering this question. But figuring out which hominin species was present when at the cave and which artifacts they made has proved challenging. Now new efforts to date the remains from Denisova are at last bringing that picture into sharper focus. Two studies published in the January 31 Nature provide a time line of human occupation of the cave. The results raise intriguing questions about the origins of symbolism and certain technologies traditionally considered to be inventions of Homo sapiens alone.

Archaeologists have been unearthing artifacts from Denisova Cave since the 1980s. The site contains frustratingly little in the way of hominin fossils, however. Most of the bones from the site are mere scraps, too incomplete to assign to a particular species on the basis of their physical characteristics. But in the last decade researchers have managed to recover ancient DNA from some of these fossil bits and from sediments in the cave. The DNA shows both Neandertals and another archaic group known as the Denisovans hung out there. And last year a team reported they had retrieved DNA from what was apparently a hybrid individual who had a Neandertal mom and a Denisovan dad. But for all that scientists have been able to piece together about Denisova, the timing of hominin occupation of the site has remained uncertain, thanks to certain quirks of site formation and preservation as well as the limitations of various techniques used to date archaeological and fossil material.


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In the new studies, two groups of researchers obtained a raft of fresh dates for the stratigraphic levels of interest at the site using a combination of techniques. One group, led by Zenobia Jacobs and Bo Li of the University of Wollongong in Australia, used a method called optically stimulated luminescence to date sediments from the cave. The team also reconstructed the environmental conditions at the site between 300,000 and 20,000 years ago. In the second study, Katerina Douka of the Max Planck Institute for the Science of Human History in Germany, Thomas Higham of the University of Oxford and their colleagues used radiocarbon dating to ascertain the ages of artifacts spanning the transition from the simpler Middle Paleolithic material culture to the more elaborate Upper Paleolithic one. Most of the human fossils are too old for radiocarbon dating, which maxes out at around 50,000 years. So the team determined the so-called relative genetic ages of the human fossils from the site by comparing their DNA sequences with those obtained from other human fossils and counting the differences between them. Such mutations accumulate at a known rate in modern humans. Using that rate the researchers were able to convert the ancient DNA differences to time. Douka, Higham and their colleagues then fed all of the ages obtained from the radiocarbon and optically stimulated luminescence methods, along with timing data from the genetic studies and the stratigraphic layers themselves, into a statistical model that calculated the most probable ages for the human fossils.

The results of these studies reveal Denisovans and Neandertals occupied the cave intermittently from at least 200,000 until around 50,000 years ago during both cooler and warmer climate phases. Denisovans were the first of the two groups to move into the cave and the last to abandon it. They probably overlapped there around 120,000 years ago, and possibly at other times as well.

The time line hints at a tantalizing possibility for who made the early Upper Paleolithic artifacts at the site, which include animal tooth pendants, a stunning stone bracelet and a needle and other tools crafted from bone. The radiocarbon dates obtained from some of the pendants and bone tools put them at 43,000 to 49,000 years old. There are no known hominin remains of that age from the site—the youngest specimen is a Denisovan fossil that dates to between 52,000 and 76,000 years ago. Yet Douka, Higham and their colleagues think creators of these artifacts are likely to have been Denisovans. Neandertals appear to have checked out of the cave by around 80,000 years ago. A fossil from the site of Ust’ Ishim documents the presence of our species in western Siberia around 45,000 years ago, which is the right time for it to be the maker of these artifacts. But that site is hundreds of kilometers from Denisova. “Our Russian colleagues have rightfully argued that we have no modern human fossils at Denisova and no modern human DNA from Denisova sediments, so why invoke modern humans” to explain the onset of the Upper Paleolithic at the site, Douka says. “One might say that given [the Ust’ Ishim fossil], we should assume modern humans made the pendants and bone tools at Denisova, but we don’t have modern human fossils in the Altai at that time.” Higham adds: “It could be modern humans but the most parsimonious explanation for the moment is that it’s Denisovans.”

The suggestion Denisovans developed the Upper Paleolithic artifacts at the site bears on a hot topic in paleoanthropology: the origins of modern behavior and cognition. Once upon a time, archaeologists thought only H. sapiens made symbolic items such as jewelry and advanced technology such as standardized bone tools. Then discoveries in the 1970s ignited debate over whether Neandertals also might have invented such items. In recent years evidence has mounted in support of a more sophisticated Neandertal. For instance, last year researchers reported cave paintings in Spain pre-date the arrival of H. sapiens to the region by thousands of years and must therefore be Neandertals’ handiwork. Neandertals, however, are not the only archaic hominin species to show signs of advanced cognition: In 2015 archaeologists unveiled their discovery of a shell that was engraved with a geometric design some 500,000 years ago—long before the origin of modern humans or Neandertals—the implication being that an earlier human ancestor known from this time period, Homo erectus, must have been the designer.

Could Denisovans have independently developed modern cognitive capabilities, too? Archaeologist Francesco d’Errico of the University of Bordeaux in France, who was not involved in the new studies, contends the paucity of relevant archaeological material from the site and insufficient description of these remains “make it difficult to reach a firm conclusion.” But “I’m not against the idea,” he says. “I do not see why archaic hominins could have not invented personal ornamentation independently and repeatedly, and a lot of evidence from Europe is now supporting this view.”

Pendants made from animal teeth and tools fashioned from bone may have been manufactured by Denisovans. Credit: Katerina Douka