
Ancient protein from pre-human teeth reveals genetic secrets of human evolutionary tree
Researchers have extracted 2 million-year-old protein remains from ancient pre-human teeth to reveal biological sex and genetic variability.
The teeth are from Paranthropus robustus, an extinct hominin genus that emerged and evolved in Africa between 2.8 and 1.2 Ma. It is considered to be a side branch of our evolutionary tree. It walked on two legs and co-existed with early species of Homo in Africa, possibly interacting.
The work, published in the journal Science, marks a significant breakthrough in human evolution studies. It provides some of the oldest human genetic data from Africa and reveals previously undetected genetic variability.
'Because we can sample multiple African Pleistocene hominin individuals classified within the same group, we're now able to observe not just biological sex but, for the first time, genetic differences that might have existed among them,' says the study's co-lead Palesa Madupe.
Madupe is a postdoctoral research Fellow at the Globe Institute at the University of Copenhagen and research associate at the Human Evolution Research Institute (HERI) at the University of Cape Town.
The researchers used a technique called palaeoproteomics to retrieve ancient protein sequences from the teeth of four Paranthropus robustus fossils recovered from the cave site Swartkrans.
Solving the riddle
Using state-of-the-art mass spectrometry techniques, they partially reconstructed the ancient enamel protein sequences from the teeth. They found that two of the fossils are male and two are female. But how was this done?
Madupe explains: Among the proteins found in tooth enamel, there's one called amelogenin. This protein is unique because its genetic instructions are located on the sex chromosomes: biological females have a version called amelogenin X, while biological males have both amelogenin X and amelogenin Y.
'We used mass spectrometry to detect which protein fragments are present in the fossilised teeth we are analysing. The precise detection of amelogenin Y protein fragments allows us to confidently identify that specimen as belonging to a male individual.
'The challenge comes when we only detect amelogenin X protein fragments, as this could indicate either a female or a male individual whose amelogenin Y is not measured.
'To solve this, we developed a quantitative method for increasing certainty that the lack of amelogenin Y detection proves that those individuals are females.'
Eventually, two were identified as male and two as female, just by tiny ancient proteins.
Ancient diversity
A single genetic variant in another protein, enamelin, was also identified that differentiated the four specimens from one another.
Two specimens carried one version of the protein, a third carried another and a fourth specimen appeared to carry both.
Their methodology allows for the partial recovery of the amino acid sequences of specific proteins from dental enamel.
'You can imagine this 'amino acid sequence' as a sequence of letters, with each letter corresponding to a specific amino acid [and with 20 possible letters to choose from for each position of the sequence]. An amino acid sequence is usually characteristic of a species; members of the same species will have the same sequence of letters for a protein.
'When we recovered and looked at the enamelin sequence of the four specimens, we saw that the sequences differed at one letter; they had 'a single genetic variant'.'
Ioannis Patramanis and Claire Koenig, co-leads from the University of Copenhagen, explained that there are a number of reasons this difference could have occurred. For example, it could be that Paranthropus robustus has a high genetic diversity, or that the four samples belong to different populations or subspecies of Paranthropus, or that we sampled the same species but at different time points in its evolution.
'When studying proteins, specific mutations are thought to be characteristic of a species and, as such, used to identify it. We were thus quite surprised to discover that what we initially thought was a mutation uniquely describing Paranthropus robustus, was actually variable within that group; some individuals had it while others did not,' says Patramanis.
The future and DNA
HERI co-director Rebecca Ackermann was a senior author on the study, with contributions from co-director Robyn Pickering and several HERI research associates.
'Being able to accurately determine the sex of ancient fossils is a big breakthrough as it allows us to determine whether the variation we see in a sample is due to sexual dimorphism or other factors such as taxonomic diversity,' says Ackermann.
'This has the potential to help us understand sex-related differences in morphology and behaviour. It also provides some control for determining how many species are being sampled. It also may provide direct evidence for understanding the hominin family tree, though this is based on a very small amount of genetic information, so we need to be very cautious in these interpretations.
'Palaeoproteomics does give us insight into genetics, as DNA encodes proteins, so we can work backwards to reconstruct DNA sequences.
'But it's important to remember that the enamel proteome is very small, so this is just a tiny bit of genetic information. At this point, ancient proteins are our only genetic information for deep-time African fossils.
'DNA preservation is poor in African environments, and so far our time depth for understanding human evolution from ancient DNA in Africa is only about 20 thousand years. Only time will tell whether this can be pushed back further!' says Ackerman. DM
Hashtags

Try Our AI Features
Explore what Daily8 AI can do for you:
Comments
No comments yet...
Related Articles

TimesLIVE
10-07-2025
- TimesLIVE
Ancient proteins found in fossils up to 24-million years old
Scientists in recent years have made progress in finding ancient DNA in fossils, gaining insight into organisms that lived long ago. But the oldest DNA obtained so far dates back about 2-million years. Proteins, a cell's molecular machinery, also offer valuable information and have the virtue of surviving much longer, as new research shows. Scientists have now extracted and sequenced proteins from dental fossils of extinct rhinoceroses, elephants and hippopotamuses, including from a rhino tooth 21- to 24-million years old. Separate research teams found protein fragments in fossils from vastly different environments — the frigid High Arctic of Canada and the scorching Rift Valley in Kenya. 'Together, these complementary projects demonstrate that proteins — fundamental building blocks of living organisms that preserve information about evolutionary history — can be found in ancient fossils the world over,' said Harvard University evolutionary biologist Daniel Green, lead author of the Kenya fossils study published in the journal Nature. This opens a new frontier for probing the deep evolutionary past, including the human lineage and perhaps even dinosaurs. 'Ancient proteins can tell us about an organism's evolutionary history by providing molecular data from specimens too old for DNA preservation. This allows researchers to clarify evolutionary relationships across the tree of life, even for species that went extinct millions of years ago,' said Ryan Sinclair Paterson, a postdoctoral researcher at the University of Copenhagen's Globe Institute and lead author of the Canada fossil study in Nature. DNA and proteins are fragile and degrade over time, but proteins are more resilient. The oldest-known DNA is from organisms that lived in Greenland 2-million years ago. Until now, the oldest-known proteins preserved well enough to offer insight on evolutionary relationships were about 4-million years old, from the Canadian Arctic.

TimesLIVE
01-07-2025
- TimesLIVE
Rocks in Canada's Quebec province found to be the oldest on Earth
The researchers applied two dating methods based on an analysis of the radioactive decay of the elements samarium and neodymium contained in them. They produced the same conclusion, that the rocks were 4.16-billion years old. Future chemical analyses of the rocks could provide insight into Earth's conditions during the Hadean, a time shrouded in mystery because of the paucity of physical remains. 'The rocks and the Nuvvuagittuq belt being the only rock record from the Hadean, they offer a unique window into our planet's earliest time to better understand how the first crust formed on Earth and what were the geodynamic processes involved,' said University of Ottawa geology professor Jonathan O'Neil, who led the study published on Thursday in the journal Science. The rocks may have formed when rain fell on molten rock, cooling and solidifying it. The rain would have been composed of water evaporated from Earth's primordial seas. 'Since some of the rocks were also formed from precipitation from ancient seawater, they can shed light on temperatures and the first oceans' composition and help establish the environment where life could have begun on Earth,' O'Neil said. Until recently, the oldest known rocks were ones dating to about 4.03-billion years ago from Canada's Northwest Territories, O'Neil said. While the Nuvvuagittuq samples are the oldest known rocks, tiny crystals of the mineral zircon from western Australia have been dated to 4.4-billion years old. The Hadean ran from Earth's formation roughly 4.5-billion years ago until 4.03-billion years ago. Early during this eon, a huge collision occurred that is believed to have resulted in the formation of the moon. However, by the time the Nuvvuagittuq rocks formed, Earth had begun to become a more recognisable place. 'The Earth was not a big ball of molten lava during the entire Hadean eon, as its name would suggest. By nearly 4.4-billion years ago, a rocky crust existed on Earth, likely mostly basaltic and covered with shallow and warmer oceans. An atmosphere was present, but different from the present day atmosphere,' O'Neil said. There had been some controversy over the age of the Nuvvuagittuq rocks. As reported in a study published in 2008, previous tests on samples from the volcanic rock layers that contained the intrusions yielded conflicting dates, one giving an age of 4.3-billion years and another giving a younger age of 3.3-billion to 3.8-billion years. O'Neil said the discrepancy may have been because the method that produced the conclusion of a younger age was sensitive to thermal events that have occurred since the rock formed, skewing the finding. The new study, with two testing methods producing harmonious conclusions on the age of the intrusion rocks, provides a minimum age for the volcanic rocks that contain the intrusions, O'Neil added. 'The intrusion would be 4.16-billion years old, and because the volcanic rocks must be older their best age would be 4.3-billion years old, as supported by the 2008 study.'


Daily Maverick
19-06-2025
- Daily Maverick
New research strengthens case for age of ancient New Mexico footprints
Researchers used a technique called radiocarbon dating to determine that organic matter in the remains of wetland muds and shallow lake sediments near the fossilized foot impressions is between 20,700 and 22,400 years old. That closely correlates to previous findings, based on the age of pollen and seeds at the site, that the tracks are between 21,000 and 23,000 years old. The footprints, whose discovery was announced in 2021, indicate that humans trod the landscape of North America thousands of years earlier than previously thought, during the most inhospitable conditions of the last Ice Age, a time called the last glacial maximum. The age of the footprints has been a contentious issue. Asked how the new findings align with the previous ones, University of Arizona archaeologist and geologist Vance Holliday, the study leader, replied: 'Spectacularly well.' Homo sapiens arose in Africa roughly 300,000 years ago and later spread worldwide. Scientists believe our species entered North America from Asia by trekking across a land bridge that once connected Siberia to Alaska. Previous archaeological evidence had suggested that human occupation of North America started roughly 16,000 years ago. The hunter-gatherers who left the tracks were traversing the floodplain of a river that flowed into an ancient body of water called Lake Otero. The mud through which they walked included bits of semi-aquatic plants that had grown in these wetlands. Radiocarbon dating is used to determine the age of organic material based on the decay of an isotope called carbon-14, a variant of the element carbon. Living organisms absorb carbon-14 into their tissue. After an organism dies, this isotope changes into other atoms over time, providing a metric for determining age. 'Three separate carbon sources – pollen, seeds and organic muds and sediments – have now been dated by different radiocarbon labs over the course of the trackway research, and they all indicate a last glacial maximum age for the footprints,' said Jason Windingstad, a University of Arizona doctoral candidate in environmental science and co-author of the study published this week in the journal Science Advances. The original 2021 study dated the footprints using radiocarbon dating on seeds of an aquatic plant called spiral ditchgrass found alongside the tracks. A study published in 2023 used radiocarbon dating on conifer pollen grains from the same sediment layers as the ditchgrass seeds. But some scientists had viewed the seeds and pollen as unreliable markers for dating the tracks. The new study provides further corroboration of the dating while also giving a better understanding of the local landscape at the time. 'When the original paper appeared, at the time we didn't know enough about the ancient landscape because it was either buried under the White Sands dune field or was destroyed when ancient Lake Otero, which had a lot of gypsum, dried out after the last Ice Age and was eroded by the wind to create the dunes,' Holliday said. Today, the landscape situated just west of the city of Alamogordo consists of rolling beige-colored dunes of the mineral gypsum. 'The area of and around the tracks included water that came off the mountains to the east, the edge of the old lake and wetlands along the margins of the lake. Our dating shows that this environment persisted before, during and after the time that people left their tracks,' Holliday said. The area could have provided important resources for hunter-gatherers. 'We know from the abundant tracks in the area that at least mammoths, giant ground sloths, camels and dire wolves were around, and likely other large animals. Given the setting, there must have been a large variety of other animals and also plants,' Holliday added. The climate was markedly different than today, with cooler summers and the area receiving significantly more precipitation. 'It is important to note that this is a trackway site, not a habitation site,' Windingstad said. 'It provides us a narrow view of people traveling across the landscape. Where they were going and where they came from is obviously an open question and one that requires the discovery and excavation of sites that are of similar age in the region. So far, these have not been found.'