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Daily Maverick
6 days ago
- Science
- Daily Maverick
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. 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
CNN
10-04-2025
- Science
- CNN
Jawbone dredged up from the seafloor expands the range of a mysterious species of ancient human
Summary Scientists have identified a fossilized jawbone found off Taiwan's coast as belonging to a Denisovan man. Researchers confirmed the ancient human's identity by analyzing protein fragments in teeth attached to the jaw. This discovery marks the third confirmed location where Denisovans lived, spanning diverse environments across Asia. Denisovans were first identified in 2010 from DNA extracted from a finger bone in Siberia. The mysterious humans don't have a widely accepted official species name yet. A fossilized jawbone dredged up by a fishing net from the seafloor 15 ½ miles (25 kilometers) off the coast of Taiwan in 2010 looked human, but for years scientists failed to nail down exactly where it fit in the human family tree. Now, scientists have been able to confirm the identity of the mystery fossil, known as Penghu 1, through analyzing ancient protein fragments contained in teeth still attached to the jaw. The jawbone belonged to a Denisovan man, according to the findings published Thursday in the journal Science. 'We've determined and shown over the past couple of years that these proteins can survive longer than DNA does, and that if we have decent recovery, we can say something about the evolutionary ancestry of a specimen,' said study coauthor Frido Welker, an associate professor of biomolecular paleoanthropology at the University of Copenhagen's Globe Institute in Denmark. Fishermen working off the coast of Taiwan long have dredged up the bones of ancient animals — elephants, water buffalo and hyenas — in their nets, relics of an ice age past when sea levels were lower and the ocean channel was a land bridge. The Denisovan man likely lived on this strip of land that once existed between what's now China and Taiwan. This discovery establishes the third place that the enigmatic ancient humans first identified in 2010 were definitively known to have lived and shows that the Denisovans occupied a diverse range of environments: Siberian mountains, the high-altitude Tibetan Plateau and the humid subtropical latitudes, Welker added. Fishermen who find fossils among their catch often sell their finds to antique shops, where collectors pick them up, said study coauthor Chun-Hsiang Chang, a curator of paleontology at Taiwan's National Museum of Natural Science. The museum has thousands of fossils found from the seabed in its collection. One collector brought the jawbone, now identified as Denisovan, to the museum wanting to know more about the specimen, and Chang said he immediately realized it was unusual and encouraged the collector to donate or sell the fossil to the museum, which he did. A paper Chang coauthored in 2015 argued the fossil belonged to the genus Homo, the grouping to which our species, Homo sapiens, and other ancient humans such as Neanderthals belong, but colleagues were not able to extract any ancient DNA from the fossil and couldn't verify the exact species. It also wasn't possible to date the fossil accurately. Scientists believe it has an age range of between 10,000 and 70,000 or 130,000 and 190,000 years old, dating the bone to a time when past sea levels in that vicinity were low. Chang took the specimen to Copenhagen in 2022 hoping to learn more from Welker and other scientists who were pioneering techniques to extract proteins from fossils, a field known as paleoproteomics. Chang recalled airport security in Copenhagen stopping him when the case containing the jawbone passed through an X-ray machine. 'They stopped me and wanted me to open (the case),' he said. 'I thought maybe they were going to arrest me.' Chang said he was allowed to leave only after sharing his credentials and giving the security personnel 'a very short human evolution lesson.' Before testing the jawbone, Welker and his colleagues sampled an elephant bone and pig bone from the same part of the seabed to work out which extraction methods would work best and determine whether proteins were still present. The team found proteins and proceeded with extracting them. Two amino acid sequences from the proteins recovered from the specimen matched those known from the Denisovan genome — a complete set of genetic information sequenced from DNA. What's more, the lab work detected a type of protein with a sex-specific peptide called amelogenin, and Y-chromosome specific peptides revealed that the Denisovan individual was male, Welker said. Denisovans were first identified in 2010 in a lab using DNA sequences extracted from a tiny fragment of finger bone found in Denisova Cave in Siberia's Altai Mountains, which is how the group got its name. Genetic analysis subsequently revealed that the Denisovans, like Neanderthals, had once interbred with early modern humans. Traces of Denisovan DNA found in present-day people suggest the ancient species likely once lived across much of Asia, and the recent discovery of Denisovan fossils from outside their namesake cave has begun to show they occupied a wide range of places in Asia. In 2019, scientists shared news that a jawbone found in a cave on the northeastern edge of the Tibetan Plateau, known as the Xiahe mandible, contained a Denisovan molecular signature. A Denisovan rib bone from the same cave was reported in 2024. In 2022, scientists identified a tooth unearthed at a cave in Laos as Denisovan because it closely resembled the tooth from the Xiahe mandible. The clue placed the species in Southeast Asia for the first time, though scientists were not able to get any definitive molecular information from the molar to confirm it. The good preservation of the proteins in the Penghu 1 mandible is surprising, given that it had been at the bottom of the sea for a long time, said archaeologist Zhang Dongju, a professor at China's Lanzhou University who worked on the Xiahe jawbone. She was not involved in the study. 'With the accumulation of Denisovan fossils and the increase of Denisovan-specific molecular signature identified, identification of Denisovan fossils will be easier,' she said. 'And I believe more Denisovan fossils will be found and identified in (the) future. And we will know more about this mysterious species.' Katerina Douka, an associate professor in archaeological science at Austria's University of Vienna, described Denisovans as a paradox because scientists have detailed genetic information about the species but few fossils, so little is known about how they looked, although she noted they had 'exceptionally large' molars. The Penghu 1 and Xiahe mandibles did not have wisdom teeth, which could indicate that their jaws did not protrude forward in their face, said Ryan McRae, a paleoanthropologist at the Smithsonian National Museum of Natural History in Washington, DC. 'Neither mandible has a chin, like modern humans do, so the front of their jawline would probably look flatter than ours,' McRae said by email. 'The authors wisely point out that the Penghu mandible is male, which means that it may exhibit the larger, more robust end of variation for this species. In other words, female Denisovans could look the same, or quite different, we just don't know yet.' Douka and McRae weren't involved in the study. The mysterious humans don't have a widely accepted official species name yet, although some scientists have suggested Homo juluensis, a classification that groups Denisovan fossils with other fossils from China, including 'dragon man,' a skull described in 2021. Chang said that he and his colleagues hope to revisit the 4,000 or so fossils in the National Museum of Natural Science's collection that have been gathered from the seabed in the Taiwan Strait over the past 40 to 50 years and use the same proteomic methods applied to the Penghu 1 jawbone to investigate whether any other fragments belong to Denisovans. 'Maybe inside my collection there's some treasure we don't know about,' Chang said.
CNN
10-04-2025
- Science
- CNN
Jawbone dredged up from the seafloor expands the range of a mysterious species of ancient human
Summary Scientists have identified a fossilized jawbone found off Taiwan's coast as belonging to a Denisovan man. Researchers confirmed the ancient human's identity by analyzing protein fragments in teeth attached to the jaw. This discovery marks the third confirmed location where Denisovans lived, spanning diverse environments across Asia. Denisovans were first identified in 2010 from DNA extracted from a finger bone in Siberia. The mysterious humans don't have a widely accepted official species name yet. A fossilized jawbone dredged up by a fishing net from the seafloor 15 ½ miles (25 kilometers) off the coast of Taiwan in 2010 looked human, but for years scientists failed to nail down exactly where it fit in the human family tree. Now, scientists have been able to confirm the identity of the mystery fossil, known as Penghu 1, through analyzing ancient protein fragments contained in teeth still attached to the jaw. The jawbone belonged to a Denisovan man, according to the findings published Thursday in the journal Science. 'We've determined and shown over the past couple of years that these proteins can survive longer than DNA does, and that if we have decent recovery, we can say something about the evolutionary ancestry of a specimen,' said study coauthor Frido Welker, an associate professor of biomolecular paleoanthropology at the University of Copenhagen's Globe Institute in Denmark. Fishermen working off the coast of Taiwan long have dredged up the bones of ancient animals — elephants, water buffalo and hyenas — in their nets, relics of an ice age past when sea levels were lower and the ocean channel was a land bridge. The Denisovan man likely lived on this strip of land that once existed between what's now China and Taiwan. This discovery establishes the third place that the enigmatic ancient humans first identified in 2010 were definitively known to have lived and shows that the Denisovans occupied a diverse range of environments: Siberian mountains, the high-altitude Tibetan Plateau and the humid subtropical latitudes, Welker added. Fishermen who find fossils among their catch often sell their finds to antique shops, where collectors pick them up, said study coauthor Chun-Hsiang Chang, a curator of paleontology at Taiwan's National Museum of Natural Science. The museum has thousands of fossils found from the seabed in its collection. One collector brought the jawbone, now identified as Denisovan, to the museum wanting to know more about the specimen, and Chang said he immediately realized it was unusual and encouraged the collector to donate or sell the fossil to the museum, which he did. A paper Chang coauthored in 2015 argued the fossil belonged to the genus Homo, the grouping to which our species, Homo sapiens, and other ancient humans such as Neanderthals belong, but colleagues were not able to extract any ancient DNA from the fossil and couldn't verify the exact species. It also wasn't possible to date the fossil accurately. Scientists believe it has an age range of between 10,000 and 70,000 or 130,000 and 190,000 years old, dating the bone to a time when past sea levels in that vicinity were low. Chang took the specimen to Copenhagen in 2022 hoping to learn more from Welker and other scientists who were pioneering techniques to extract proteins from fossils, a field known as paleoproteomics. Chang recalled airport security in Copenhagen stopping him when the case containing the jawbone passed through an X-ray machine. 'They stopped me and wanted me to open (the case),' he said. 'I thought maybe they were going to arrest me.' Chang said he was allowed to leave only after sharing his credentials and giving the security personnel 'a very short human evolution lesson.' Before testing the jawbone, Welker and his colleagues sampled an elephant bone and pig bone from the same part of the seabed to work out which extraction methods would work best and determine whether proteins were still present. The team found proteins and proceeded with extracting them. Two amino acid sequences from the proteins recovered from the specimen matched those known from the Denisovan genome — a complete set of genetic information sequenced from DNA. What's more, the lab work detected a type of protein with a sex-specific peptide called amelogenin, and Y-chromosome specific peptides revealed that the Denisovan individual was male, Welker said. Denisovans were first identified in 2010 in a lab using DNA sequences extracted from a tiny fragment of finger bone found in Denisova Cave in Siberia's Altai Mountains, which is how the group got its name. Genetic analysis subsequently revealed that the Denisovans, like Neanderthals, had once interbred with early modern humans. Traces of Denisovan DNA found in present-day people suggest the ancient species likely once lived across much of Asia, and the recent discovery of Denisovan fossils from outside their namesake cave has begun to show they occupied a wide range of places in Asia. In 2019, scientists shared news that a jawbone found in a cave on the northeastern edge of the Tibetan Plateau, known as the Xiahe mandible, contained a Denisovan molecular signature. A Denisovan rib bone from the same cave was reported in 2024. In 2022, scientists identified a tooth unearthed at a cave in Laos as Denisovan because it closely resembled the tooth from the Xiahe mandible. The clue placed the species in Southeast Asia for the first time, though scientists were not able to get any definitive molecular information from the molar to confirm it. The good preservation of the proteins in the Penghu 1 mandible is surprising, given that it had been at the bottom of the sea for a long time, said archaeologist Zhang Dongju, a professor at China's Lanzhou University who worked on the Xiahe jawbone. She was not involved in the study. 'With the accumulation of Denisovan fossils and the increase of Denisovan-specific molecular signature identified, identification of Denisovan fossils will be easier,' she said. 'And I believe more Denisovan fossils will be found and identified in (the) future. And we will know more about this mysterious species.' Katerina Douka, an associate professor in archaeological science at Austria's University of Vienna, described Denisovans as a paradox because scientists have detailed genetic information about the species but few fossils, so little is known about how they looked, although she noted they had 'exceptionally large' molars. The Penghu 1 and Xiahe mandibles did not have wisdom teeth, which could indicate that their jaws did not protrude forward in their face, said Ryan McRae, a paleoanthropologist at the Smithsonian National Museum of Natural History in Washington, DC. 'Neither mandible has a chin, like modern humans do, so the front of their jawline would probably look flatter than ours,' McRae said by email. 'The authors wisely point out that the Penghu mandible is male, which means that it may exhibit the larger, more robust end of variation for this species. In other words, female Denisovans could look the same, or quite different, we just don't know yet.' Douka and McRae weren't involved in the study. The mysterious humans don't have a widely accepted official species name yet, although some scientists have suggested Homo juluensis, a classification that groups Denisovan fossils with other fossils from China, including 'dragon man,' a skull described in 2021. Chang said that he and his colleagues hope to revisit the 4,000 or so fossils in the National Museum of Natural Science's collection that have been gathered from the seabed in the Taiwan Strait over the past 40 to 50 years and use the same proteomic methods applied to the Penghu 1 jawbone to investigate whether any other fragments belong to Denisovans. 'Maybe inside my collection there's some treasure we don't know about,' Chang said.
