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]

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]

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]