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Yahoo
3 days ago
- General
- Yahoo
2.2 million-year-old teeth reveal secrets of human relatives found in a South African cave
When you buy through links on our articles, Future and its syndication partners may earn a commission. Small pieces of tooth enamel from deep in a South African cave have begun to reveal secrets held for 2 million years by a distant human relative, a new study finds.. Archaeologists recovered teeth from four members of the species Paranthropus robustus, a two-legged human relative who lived between 1.8 million and 1.2 million years ago, from Swartkrans, a fossil-bearing cave in Africa's Cradle of Humankind World Heritage site. Using cutting-edge techniques that can analyze fossils' amino acid sequences, the researchers were able to determine the sex of the individuals and discovered surprising genetic variation that could point to the existence of a previously unknown species. These techniques are part of the field of proteomics, or studying sets of preserved proteins — a relatively new area of science that is shedding much-needed light on the evolution of early hominins, a group that includes humans and our closest relatives. "Figuring out the human family tree using proteins is the goal," Claire Koenig, a postdoctoral researcher at the University of Copenhagen and co-author of a study published Thursday (May 29) in the journal Science, told Live Science in an email co-written with lead author Palesa Madupe and co-author Ioannis Patramanis. But currently "our ability to distinguish between different species is limited by the small number of different proteins present in enamel." Although DNA has been recovered from ancient skeletons in Africa, so far that technique has only successfully worked on hominin material dating to no more than 20,000 years ago — well within the lifetime of our own species, Homo sapiens — because DNA degrades quickly in that environment. To get at the roughly 6 million-year history of hominin evolution, analysis of the harder and more stable tissue of dental enamel is needed. In the new study, an international team of researchers led by Madupe employed paleoproteomic analysis to move beyond the limits of ancient DNA and understand the genes of four hominins who lived around 2 million years ago. "Proteomics is inherently a destructive technique, but we take great care to minimize impact, especially when working with rare or precious specimens," Koenig said. Related: In a 1st, ancient proteins reveal sex of human relative from 3.5 million years ago The researchers focused their proteomic analysis on four P. robustus individuals who likely all died around the same time. They were able to identify AMELY-specific peptides, which are found in the tooth enamel of males, in two individuals. The other two individuals had a high AMELX intensity, meaning they were likely female. Correctly determining the sex of a fossil is important in paleoanthropology because most hominins are sexually dimorphic, with males being, on average, larger than females. Experts therefore expect that any species will have some larger and some smaller individuals. But Madupe and colleagues discovered a surprising result: one P. robustus individual who was thought to be female, based on tooth size and shape, was actually male, based on proteomic data. "Our results thus indicate that measurements of dental size are not necessarily accurate for correct sex estimation," the researchers wrote in the study. Since sex alone could not explain the differences in the appearance of P. robustus, the team investigated whether the diversity they were seeing could be the result of different groups or species they didn't know about, or the result of interbreeding, as P. robustus overlapped in time with australopithecines and early members of the Homo genus. The researchers found a couple amino acid sequence positions that varied among the P. robustus specimens they examined, and that were different from the amino acid sequences seen in present-day humans, Neanderthals and Denisovans. This analysis revealed that one of the individuals — SK-835, whose molecular sex and morphological sex did not match up — was more distantly related to the other three individuals than they were to each other. "It would be premature to classify SK-835 as a member of the newly proposed Paranthropus [capensis] taxa," Koenig said, but it remains a possibility that the amino acid difference reflects its position in a different species than the rest. It could also be explained, however, by microevolution at different sites, study co-author Rebecca Ackermann, a biological anthropologist at the University of Cape Town, told Live Science in an email. "We need to analyse more Paranthropus material from different sites to get a better handle on the variation within southern African Paranthropus," she said. RELATED STORIES —Smallest human relative ever found may have been devoured by a leopard 2 million years ago —What's the oldest known case of cancer in humans? —World's oldest human DNA found in 800,000-year-old tooth of a cannibal Because the enamel proteome is so much smaller — and provides less information — than a full genome, reconstructions of fossil human relatives need to be cautiously interpreted, Ackermann said. Koenig expects that further methodological developments will be beneficial, including less invasive methods such as acid etching to remove an extremely thin layer of dental enamel, and the development of faster and more sensitive protein-sequencing instruments. "It remains to be seen, for example, whether or not we can molecularly tell apart a Paranthropus robustus from an Australopithecus africanus," Koenig said, "because these species are closely related and therefore their proteins are going to look very similar."
Daily Maverick
3 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
