̽��ֱ�� of Cambridge - Richard Durbin

Genetic study reveals hidden chapter in human evolution

sc604 — Tue, 18 Mar 2025 10:00:00 +0000

Using advanced analysis based on full genome sequences, researchers from the ̽��ֱ�� of Cambridge have found evidence that modern humans are the result of a genetic mixing event between two ancient populations that diverged around 1.5 million years ago. About 300,000 years ago, these groups came back together, with one group contributing 80% of the genetic makeup of modern humans and the other contributing 20%.

For the last two decades, the prevailing view in human evolutionary genetics has been that Homo sapiens first appeared in Africa around 200,000 to 300,000 years ago, and descended from a single lineage. However, these latest results, reported in the journal Nature Genetics, suggest a more complex story.

“ ̽��ֱ��question of where we come from is one that has fascinated humans for centuries,” said first author Dr Trevor Cousins from Cambridge’s Department of Genetics. “For a long time, it’s been assumed that we evolved from a single continuous ancestral lineage, but the exact details of our origins are uncertain.”

“Our research shows clear signs that our evolutionary origins are more complex, involving different groups that developed separately for more than a million years, then came back to form the modern human species,” said co-author Professor Richard Durbin, also from the Department of Genetics.

While earlier research has already shown that Neanderthals and Denisovans – two now-extinct human relatives – interbred with Homo sapiens around 50,000 years ago, this new research suggests that long before those interactions – around 300,000 years ago – a much more substantial genetic mixing took place. Unlike Neanderthal DNA, which makes up roughly 2% of the genome of non-African modern humans, this ancient mixing event contributed as much as 10 times that amount and is found in all modern humans.

̽��ֱ��team’s method relied on analysing modern human DNA, rather than extracting genetic material from ancient bones, and enabled them to infer the presence of ancestral populations that may have otherwise left no physical trace. ̽��ֱ��data used in the study is from the 1000 Genomes Project, a global initiative that sequenced DNA from populations across Africa, Asia, Europe, and the Americas.

̽��ֱ��team developed a computational algorithm called cobraa that models how ancient human populations split apart and later merged back together. They tested the algorithm using simulated data and applied it to real human genetic data from the 1000 Genomes Project.

While the researchers were able to identify these two ancestral populations, they also identified some striking changes that happened after the two populations initially broke apart.

“Immediately after the two ancestral populations split, we see a severe bottleneck in one of them—suggesting it shrank to a very small size before slowly growing over a period of one million years,” said co-author Professor Aylwyn Scally, also from the Department of Genetics. “This population would later contribute about 80% of the genetic material of modern humans, and also seems to have been the ancestral population from which Neanderthals and Denisovans diverged.”

̽��ֱ��study also found that genes inherited from the second population were often located away from regions of the genome linked to gene functions, suggesting that they may have been less compatible with the majority genetic background. This hints at a process known as purifying selection, where natural selection removes harmful mutations over time.

“However, some of the genes from the population which contributed a minority of our genetic material, particularly those related to brain function and neural processing, may have played a crucial role in human evolution,” said Cousins.

Beyond human ancestry, the researchers say their method could help to transform how scientists study the evolution of other species. In addition to their analysis of human evolutionary history, they applied the cobraa model to genetic data from bats, dolphins, chimpanzees, and gorillas, finding evidence of ancestral population structure in some but not all of these.

“What’s becoming clear is that the idea of species evolving in clean, distinct lineages is too simplistic,” said Cousins. “Interbreeding and genetic exchange have likely played a major role in the emergence of new species repeatedly across the animal kingdom.”

So who were our mysterious human ancestors? Fossil evidence suggests that species such as Homo erectus and Homo heidelbergensis lived both in Africa and other regions during this period, making them potential candidates for these ancestral populations, although more research (and perhaps more evidence) will be needed to identify which genetic ancestors corresponded to which fossil group.

Looking ahead, the team hopes to refine their model to account for more gradual genetic exchanges between populations, rather than sharp splits and reunions. They also plan to explore how their findings relate to other discoveries in anthropology, such as fossil evidence from Africa that suggests early humans may have been far more diverse than previously thought.

“ ̽��ֱ��fact that we can reconstruct events from hundreds of thousands or millions of years ago just by looking at DNA today is astonishing,” said Scally. “And it tells us that our history is far richer and more complex than we imagined.”

̽��ֱ��research was supported by Wellcome. Aylwyn Scally is a Fellow of Darwin College, Cambridge. Trevor Cousins is a member of Darwin College, Cambridge.

Reference:
Trevor Cousins, Aylwyn Scally & Richard Durbin. ‘A structured coalescent model reveals deep ancestral structure shared by all modern humans.’ Nature Genetics (2025). DOI: 10.1038/s41588-025-02117-1

Modern humans descended from not one, but at least 2 ancestral populations that drifted apart and later reconnected, long before modern humans spread across the globe.

Our history is far richer and more complex than we imagined

Aylwyn Scally

Jose A Bernat Bacete via Getty Images

Plaster reconstructions of the skulls of human ancestors

̽��ֱ��text in this work is licensed under a Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International License. Images, including our videos, are Copyright © ̽��ֱ�� of Cambridge and licensors/contributors as identified. All rights reserved. We make our image and video content available in a number of ways – on our main website under its Terms and conditions, and on a range of channels including social media that permit your use and sharing of our content under their respective Terms.

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Stone Age bear genome reconstructed from DNA in Mexican cave

jg533 — Mon, 19 Apr 2021 16:30:09 +0000

A team of scientists led by Professor Eske Willerslev in the ̽��ֱ�� of Cambridge’s Department of Zoology and the Lundbeck Foundation GeoGenetics Centre, ̽��ֱ�� of Copenhagen, have recreated the genomes of animals, plants and bacteria from microscopic fragments of DNA found in the remote Chiquihuite Cave in Mexico.

̽��ֱ��findings have been described as the ‘moon landings of genomics’, because researchers will no longer have to rely on finding and testing fossils to determine genetic ancestry and connections.

̽��ֱ��results, published today in the journal Current Biology, are the first time environmental DNA has been sequenced from soil and sediment. They include the ancient DNA profile of a Stone Age American black bear taken from samples in the cave.

Working with highly fragmented DNA from soil samples means scientists no longer have to rely on DNA samples from bone or teeth for enough genetic material to recreate a profile of ancient DNA.

̽��ֱ��samples included faeces and droplets of urine from an ancestor of the American black bear, which allowed the scientists to recreate the entire genetic code of two species of the animal: the Stone Age American black bear, and a short-faced bear called Arctodus simus that died out 12,000 years ago.

Professor Willerslev said: “When an animal or a human urinates or defecates, cells from the organism are also excreted. We can detect the DNA fragments from these cells in the soil samples and have now used these to reconstruct genomes for the first time. We have shown that hair, urine and faeces all provide genetic material which, in the right conditions, can survive for much longer than 10,000 years.

“Analysis of DNA found in soil could have the potential to expand the narrative about everything from the evolution of species to developments in climate change – fossils will no longer be needed.”

Chiquihuite Cave is a high-altitude site, situated 2,750 metres above sea level. DNA of mice, black bears, rodents, bats, voles and kangaroo rats was also found. ̽��ֱ��scientists say that DNA fragments in sediment will now be able to be tested in many former Stone Age settlements around the world.

Professor Willerslev said: “Imagine the stories those traces could tell. It’s a little insane – but also fascinating – to think that, back in the Stone Age, these bears urinated and defecated in the Chiquihuite Cave and left us the traces we’re able to analyse today.”

Reference

Petersen, M.K. et al, Environmental genomics of Late Pleistocene black bears and giant short-faced bears. Current Biology, April 2021. DOI: 10.1016/j.cub.2021.04.027

Adapted from a press release by St John's College, Cambridge.

Scientists have reconstructed ancient DNA from soil for the first time, in an advance that will significantly enhance the study of animal, plant and microorganism evolution.

Analysis of DNA found in soil could have the potential to expand the narrative about everything from the evolution of species to developments in climate change – fossils will no longer be needed.

Eske Willerslev

Devlin A Gandy

Assistant Professor Mikkel Winther Pedersen with team members sampling the different cultural layers in the cave.

̽��ֱ��text in this work is licensed under a Creative Commons Attribution 4.0 International License. Images, including our videos, are Copyright © ̽��ֱ�� of Cambridge and licensors/contributors as identified. All rights reserved. We make our image and video content available in a number of ways – as here, on our main website under its Terms and conditions, and on a range of channels including social media that permit your use and sharing of our content under their respective Terms.

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Attribution

Ambitious project launched to map genomes of all life in British Isles

jg533 — Fri, 08 Nov 2019 00:01:00 +0000

̽��ֱ��£9.4m funding will support a collaboration of ten research institutes, museums and associated organisations to launch the first phase of sequencing all the species on the British Isles. This will see the teams collect and ‘barcode’ around 8,000 key British species of animal, plant and fungi, and deliver high-quality genomes of 2,000 species.

Exploring the genomes – the entire DNA - of these species will give an unprecedented insight into how life on Earth evolved. It will uncover new genes, proteins and metabolic pathways to help develop drugs for infectious and inherited diseases.

At a time when many species are under threat from climate change and human development, the data will also help characterise, catalogue and support conservation of global biodiversity for future generations.

“This project is the start of a transformation for biological research. It will change our relationship to the natural world by enabling us to understand life as never before,” said Professor Richard Durbin in Cambridge ̽��ֱ��’s Department of Genetics, who will lead the ̽��ֱ��’s involvement in the collaboration. “It will create a knowledge resource for others to build on, just as we’ve seen with the Human Genome Project for human health.”

From the small fraction of the Earth’s species that have been sequenced, enormous advances have been made in knowledge and biomedicine. From plants, a number of lifesaving drugs have been discovered and are now being created in the lab – such as artemisinin for malaria and taxol for cancer.

Assembling the full genetic barcode of each species from the millions of genetic fragments generated in the sequencing process will rely on the ̽��ֱ�� of Cambridge’s expertise in computational analysis.

“Genome assembly is like doing a very complicated jigsaw puzzle. ̽��ֱ��genome revolution is all about information, and our ability to put the sequencing data together is based on cutting-edge computing techniques,” said Dr Shane McCarthy at the ̽��ֱ�� of Cambridge, who will work on the project with Professor Durbin.

̽��ֱ��project will identify and collect specimens that will include plants from the Cambridge ̽��ֱ�� Botanic Garden. It will set up new pipelines and workflows to process large numbers of species through DNA preparation, sequencing, assembly, gene finding and annotation. New methods will be developed for high-throughput and high-quality assembly of genomes and their annotation, and data will be shared openly through existing data sharing archives and project specific portals.

̽��ֱ��10 institutes involved in the project are:

• ̽��ֱ�� of Cambridge
• Earlham Institute (EI)
• ̽��ֱ�� of Edinburgh
• EMBL’s-European Bioinformatics Institute (EMBL-EBI)
• ̽��ֱ��Marine Biological Association (Plymouth)
• Natural History Museum
• Royal Botanic Gardens Kew
• Royal Botanic Garden Edinburgh
• ̽��ֱ�� of Oxford
• Wellcome Sanger Institute

̽��ֱ��consortium ultimately aims to sequence the genetic code of 60,000 species that live in the British Isles. Its work will act as a launchpad for a larger ambition to sequence all species on Earth, as part of the Earth Biogenome Project.

Dr Michael Dunn, Head of Genetics and Molecular Sciences at Wellcome, said, “ ̽��ֱ��mission to sequence all life on the British Isles is ambitious, but by bringing together this diverse group of organisations we believe that we have the right team to achieve it. We’ll gain new insights into nature that will help develop new treatments for infectious diseases, identify drugs to slow ageing, generate new approaches to feeding the world and create new bio-materials.”

Adapted from a press release by Wellcome.

An unprecedented insight into the diverse range of species on the British Isles will be made possible by Wellcome funding to the Darwin Tree of Life project.

This project is the start of a transformation for biological research.

Richard Durbin

Jim Haseloff

Liverwort (Pellia epiphylla)

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