First ancient DNA from West/Central Africa illuminates deep human past

An international team led by Harvard Medical School scientists has produced the first genome-wide ancient human DNA sequences from west and central Africa.

General view of the excavation of Shum Laka’s rockshelter (Grassfields region of Cameroon). This site was home to a
human population that lived in the region for at least five millennia and bore little genetic relatedness to the people
who live in the region today. Analysis of whole genome ancient DNA data from the people who lived at this site
provided insights into the existence of several never-before-appreciated, early-branching
African human lineages [Credit: Pierre de Maret, January 1994]

The data, recovered from four individuals buried at an iconic archaeological site in Cameroon between 3,000 and 8,000 years ago, enhance our understanding of the deep ancestral relationships among populations in sub-Saharan Africa, which remains the region of greatest human diversity today.

The findings, published in Nature, provide new clues in the search to identify the populations that first spoke and spread Bantu languages. The work also illuminates previously unknown "ghost" populations that contributed small portions of DNA to present-day African groups.

Map of Africa with Cameroon in dark blue and approximate location of Shum Laka marked with star. Image adapted from Alvaro1984 18/Wikimedia Commons

Research highlights:

- DNA came from the remains of two pairs of children who lived around 3,000 years ago and 8,000 years ago, respectively, during the transition from the Stone Age to the Iron Age.

- The children were buried at Shum Laka, a rock shelter in the Grassfields region of northwestern Cameroon where ancient people lived for tens of thousands of years. The site has yielded prolific artifacts along with 18 human skeletons and lies in the region where researchers suspect Bantu languages and cultures originated. The spread of Bantu languages--and the groups that spoke them--over the past 4,000 years is thought to explain why the majority of people from central, eastern and southern Africa are closely related to one another and to west/central Africans.

- Surprisingly, all four individuals are most closely related to present-day central African hunter-gatherers, who have very different ancestry from most Bantu speakers. This suggests that present-day Bantu speakers in western Cameroon and across Africa did not descend from the sequenced children's population.

Excavation of a double burial at the Shum Laka rock shelter (Grassfields region of Cameroon) containing the remains
of two boys who lived ~8,000 years ago and who were genetically from the same family. Ancient DNA reveals that
these two individuals and another pair of children buried five millennia later at Shum Laka were from a stable
 population that was then almost completely displaced by the very different populations living
in Cameroon today [Credit: Isabelle Ribot, January 1994]

- One individual's genome includes the earliest-diverging Y chromosome type, found almost nowhere outside western Cameroon today. The findings show that this oldest lineage of modern human males has been present in that region for more than 8,000 years, and perhaps much longer.

- Genetic analyses indicate that there were at least four major lineages deep in human history, between 200,000 and 300,000 years ago. This radiation hadn't been identified previously from genetic data.

- Contrary to common models, the data suggest that central African hunter-gatherers diverged from other African populations around the same time as southern African hunter-gatherers did.

- Analyses reveal another set of four branching human lineages between 60,000 and 80,000 years ago, including the lineage known to have given rise to all present-day non-Africans.

- The Shum Laka individuals themselves harbor ancestry from multiple deep lineages, including a previously unknown, early-diverging ancestry source in West Africa.

Source: Harvard Medical School [January 22, 2020]

How social structures emerge: Computer simulations uncover universality in cultural anthropology observations

What rules shaped humanity's original social networks? Researchers in Japan developed new mathematical models to understand what conditions produced traditional community structures and conventions around the world, including taboos about incest.

Illustration of communities joining through a marriage [Credit: © Caitlin Devor,
University of Tokyo, CC BY 4.0]

"We think this is the first time cultural anthropology and computer simulations have met in a single research study," said Professor Kunihiko Kaneko, an expert in theoretical biology and physics from the University of Tokyo Research Center for Complex Systems Biology.

Researchers used statistical physics and computer models common in evolutionary biology to explain the origin of common community structures documented by cultural anthropologists around the world.

The earliest social networks were tightly knit cultural groups made of multiple biologically related families. That single group would then develop relationships with other cultural groups in their local area.

In the 1960s, cultural anthropologists documented social networks of indigenous communities and identified two kinship structures common around the world. In areas with hunter-gatherer communities, anthropologists documented direct-exchange kinship structures where women from two communities change places when they marry. In areas with agrarian farming communities, kinship structures of generalized exchange developed where women move between multiple communities to marry.

"Anthropologists have documented kinship structures all over the world, but it still remains unclear how those structures emerged and why they have common properties," said Kenji Itao, a first year master's degree student in Kaneko's laboratory, whose interdisciplinary interests in physics, math and anthropology motivated this research study.

Experts in anthropology consider the incest taboo to be an extremely common social rule affecting kinship structures. The ancient incest taboo focused on social closeness, rather than genetic or blood relationships, meaning it was taboo to marry anyone born into the same cultural group.

Graphical representations of simulated social networks. Researchers used computer simulations based on principles
of statistical physics and evolutionary biology to model how human societies would form under different conditions.
Direct-exchange (left), generalized-exchange (center), and restricted-exchange (right) social structure
models observed by cultural anthropologists in the 1960s are represented graphically
[Credit: Kenji Itao, University of Tokyo, CC BY-SA 4.0]

Itao and Kaneko designed a mathematical model and computer simulation to test what external factors might cause generations of biologically related families to organize into communities with incest taboos and direct or generalized exchange of brides.

"Traditionally, it is more common for women to move to a new community when they marry, but we did not include any gender differences in this computer simulation," explained Itao.

Simulated family groups with shared traits and desires naturally grouped together into distinct cultural groups. However, the traits the group possessed were different from the traits they desired in marriage partners, meaning they did not desire spouses similar to themselves. This is the underlying cause of the traditional community-based incest taboo suggested by the study.

When the computer simulation pushed communities to cooperate, generalized exchange kinship structures arose. The simulation demonstrated different kinship structures, including the direct exchange basic structure, emerge depending on the strength of conflict to find brides and the necessity of cooperation with specific other communities.

"It is rewarding to see that the combination of statistical physics and evolution theory, together with computer simulations, will be relevant to identify universal properties that affect human societies," said Kaneko.

The current computer model is simple and only included factors of conflict and cooperation affecting marriage, but researchers hope to continue developing the model to also consider economic factors that might cause communities to separate into different classes. With these additions, the theory can hopefully be extended to explore different communities in the modern, global society.

"I would be glad if perhaps our results can give field anthropologists a hint about universal structures that might explain what they observe in new studies," said Itao.

The study is published in the Proceedings of the National Academy of Sciences.

Source: University of Tokyo [January 21, 2020]

The drawbacks of the modern face of 'Homo antecessor'

A study led by the University of Bordeaux and the Dental Anthropology Group of the Centro Nacional de Investigación sobre la Evolución Humana (CENIEH), which has been published this week in the American Journal of Physical Anthropology, reveals that the species Homo antecessor, found in level TD6 of the Gran Dolina site in the Sierra de Atapuerca (Burgos), already endured the drawbacks of having insufficient space for the third molar or wisdom tooth to erupt.

Credit: CENIEH

Analysis of the maxilla ATD6-69, "the face" of Homo antecessor, using high-resolution techniques such as micro-computed tomography carried out at the CENIEH, has enabled the identification of signs matching ectopic development, that is, outside the proper location for the third molar, and the secondary impacting pf the second molar with its retention within the alveolar bone.

"Specifically, the wisdom tooth was undergoing development upon the crown of the second molar," says Laura Martín-Francés, principal author of this study.

In this study, the hypothesis of whether the ectopic molar of this individual, whose approximate age was 10 years, was due to a combination of factors such as the characteristic modern face and the large size of the teeth of this child from Atapuerca, is discussed for the first time.

This peculiarity would have led to the lack of space for the normal development of the wisdom tooth and the consequent retention of the second molar.

"While the particular evolution in this individual is unknown, the prognosis in these cases includes the development of caries, periodontitis and even cysts. Thus, we can be sure that around one million years ago, this person would have suffered from severe toothache," affirms Martín-Francés.

For the moment, evidence of this anomaly is only known from a single individual of this species, although the imminent excavation of the entire surface of level TD6 at Gran Dolina will offer new fossil remains to find out whether this circumstance was typical of Homo antecessor due to its modern face.

Source: CENIEH [January 18, 2020]

Human-caused biodiversity decline started millions of years ago

The human-caused biodiversity decline started much earlier than researchers used to believe. According to a new study published in the scientific journal Ecology Letters the process was not started by our own species but by some of our ancestors.

Dinofelis, painting by Mauricio Antón. The picture shows a saber-toothed cat Dinofelis eating
while one of our ancestors are watching. Dinofelis has been considered a predator that our
ancestors were greatly fearing. But new research suggests that it was human ancestors that
may have caused the eventual extinction of the species along with other major predators
[Credit: University of Gothenburg]

The work was done by an international team of scientists from Sweden, Switzerland and the United Kingdom.

The researchers point out in the study that the ongoing biological diversity crisis is not a new phenomenon, but represents an acceleration of a process that human ancestors began millions of years ago.

"The extinctions that we see in the fossils are often explained as the results of climatic changes but the changes in Africa within the last few million years were relative minor and our analyses show that climatic changes were not the main cause of the observed extinctions," explains Søren Faurby, researcher at Gothenburg University and the main author of the study.

"Our analyzes show that the best explanation for the extinction of carnivores in East Africa is instead that they are caused by direct competition for food with our extinct ancestors," adds Daniele Silvestro, computational biologist and co-author of the study.

Carnivores disappeared

Our ancestors have been common throughout eastern Africa for several million years and during this time there were multiple extinctions according to Lars Werdelin, co-author and expert on African fossils.

"By investigating the African fossils, we can see a drastic reduction in the number of large carnivores, a decrease that started about 4 million years ago. About the same time, our ancestors may have started using a new technology to get food called kleptoparasitism," he explains.

Kleptoparasitism means stealing recently killed animals from other predators. For example, when a lion steals a dead antelope from a cheetah.

The researchers are now proposing, based on fossil evidence, that human ancestors stole recently killed animals from other predators. This would lead to starvation of the individual animals and over time to extinction of their entire species.

"This may be the reason why most large carnivores in Africa have developed strategies to defend their prey. For example, by picking up the prey in a tree that we see leopards doing. Other carnivores have instead evolved social behavior as we see in lions, who among other things work together to defend their prey," explains Søren Faurby

Humans today affect the world and the species that live in it more than ever before.

"But this does not mean that we previously lived in harmony with nature. Monopolization of resources is a skill we and our ancestors have had for millions of years, but only now are we able to understand and change our behavior and strive for a sustainable future. 'If you are very strong, you must also be very kind'," concludes Søren Faurby and quotes Astrid Lindgrens book about Pippi Longstocking.

Source: University of Gothenburg [January 17, 2020]

Green in tooth and claw

Hard plant foods may have made up a larger part of early human ancestors' diet than currently presumed, according to a new experimental study of modern tooth enamel from Washington University in St. Louis.

Five skull replicas of human ancestors from left to right: A. africanus, A. afarensis, H. erectus,
H. neanderthalensis and H. sapiens sapiens [Credit: Shutterstock]

Scientists often look at microscopic damage to teeth to infer what an animal was eating. This new research -- using experiments looking at microscopic interactions between food particles and enamel -- demonstrates that even the hardest plant tissues scarcely wear down primate teeth. The results have implications for reconstructing diet, and potentially for our interpretation of the fossil record of human evolution, researchers said.

"We found that hard plant tissues such as the shells of nuts and seeds barely influence microwear textures on teeth," said Adam van Casteren, lecturer in biological anthropology in Arts & Sciences, the first author of the new study in Scientific Reports. David S. Strait, professor of physical anthropology, is a co-author.

Traditionally, eating hard foods is thought to damage teeth by producing microscopic pits. "But if teeth don't demonstrate elaborate pits and scars, this doesn't necessarily rule out the consumption of hard food items," van Casteren said.

Humans diverged from non-human apes about seven million years ago in Africa. The new study addresses an ongoing debate surrounding what some early human ancestors, the australopiths, were eating. These hominin species had very large teeth and jaws, and likely huge chewing muscles.

"All these morphological attributes seem to indicate they had the ability to produce large bite forces, and therefore likely chomped down on a diet of hard or bulky food items such as nuts, seeds or underground resources like tubers," van Casteren said.

But most fossil australopith teeth don't show the kind of microscopic wear that would be expected in this scenario.

The researchers decided to test it out.

Previous mechanical experiments had shown how grit -- literally, pieces of quartz rock -- produces deep scratches on flat tooth surfaces, using a device that mimicked the microscopic interactions of particles on teeth. But there was little to no experimental data on what happens to tooth enamel when it comes in contact with actual woody plant material.

For this study, the researchers attached tiny pieces of seed shells to a probe that they dragged across enamel from a Bornean orangutan molar tooth.

They made 16 "slides" representing contacts between the enamel and three different seed shells from woody plants that are part of modern primate diets. The researchers dragged the seeds against enamel at forces comparable to any chewing action.

The seed fragments made no large pits, scratches or fractures in the enamel, the researchers found. There were a few shallow grooves, but the scientists saw nothing that indicated that hard plant tissues could contribute meaningfully to dental microwear. The seed fragments themselves, however, showed signs of degradation from being rubbed against the enamel.

This information is useful for anthropologists who are left with only fossils to try to reconstruct ancient diets.

"Our approach is not to look for correlations between the types of microscopic marks on teeth and foods being eaten -- but instead to understand the underlying mechanics of how these scars on tooth surface are formed," van Casteren said. "If we can fathom these fundamental concepts, we can generate more accurate pictures of what fossil hominins were eating."

So those big australopith jaws could have been put to use chewing on large amounts of seeds -- without scarring teeth.

"And that makes perfect sense in terms of the shape of their teeth" said Peter Lucas, a co-author at the Smithsonian Tropical Research Institute, "because the blunt low-cusped form of their molars are ideal for that purpose."

"When consuming many very small hard seeds, large bite forces are likely to be required to mill all the grains," van Casteren said. "In the light of our new findings, it is plausible that small, hard objects like grass seeds or sedge nutlets were a dietary resource for early hominins."

Source: Washington University in St. Louis [January 17, 2020]