̽��ֱ�� of Cambridge - Aylwyn Scally

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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Darwin Lectures at Cambridge ̽��ֱ�� - from evolution to REVOLUTION!

ps748 — Fri, 19 Jan 2024 09:00:58 +0000

Sir Simon Schama and Didier Queloz are among the speakers discussing the topic of revolution at the Darwin Lectures 2024.

Global human genome study reveals our complex evolutionary history

jg533 — Thu, 19 Mar 2020 14:52:52 +0000

Uncovering a large amount of previously undescribed genetic variation, the study provides new insights into our evolutionary past, and highlights the complexity of the process through which our ancestors diversified, migrated and mixed throughout the world.

Published in the journal Science, the work involved the ̽��ֱ�� of Cambridge, the Wellcome Sanger Institute, the Francis Crick Institute and other collaborators. It is the first to apply the latest high-quality sequencing technology to such a large and diverse set of humans, covering 929 genomes from 54 geographically, linguistically and culturally diverse populations from across the globe.

̽��ֱ��results provide unprecedented detail of our genetic history, and highlights how it is characterised by multiple layers of complexity. Although genetic differences between populations reflect their diversity, many patterns are shared across continents, revealing both ancient and recent connections between populations.

Researchers in the ̽��ֱ�� of Cambridge’s Department of Genetics analysed the sequencing data to investigate evidence of interbreeding between the ancestors of modern humans and extinct human lineages such as Neanderthals and Denisovans, which occurred 40,000 to 60,000 years ago.

They found evidence that the Neanderthal ancestry of modern humans can be explained by just one major ‘mixing event’, most likely involving several Neanderthal individuals coming into contact with modern humans shortly after the latter had expanded out of Africa.

"Studying the patterns of Neanderthal ancestry in present-day humans hints at the structure of human communities more than 50,000 years ago. It is remarkable that patterns of Neanderthal ancestry are so similar in populations around the world today, and may have derived from a single Neanderthal population," said Dr Aylwyn Scally, a researcher in the ̽��ֱ�� of Cambridge’s Department of Genetics who was involved in the study.

In contrast, several different sets of DNA segments inherited from Denisovans were identified in people from Oceania and East Asia, suggesting at least two distinct mixing events. “This could suggest that multiple small groups of Denisovans once lived in different regions of Asia. We expect future discoveries of ancient DNA - perhaps from other extinct humans and perhaps even inside Africa - to tell us more about ancient population structure and diversity," said Dr Ruoyun Hui at the ̽��ֱ�� of Cambridge’s Department of Genetics, who also worked on the study.

Until recently, it was thought that only people outside sub-Saharan Africa had Neanderthal DNA. Now, the discovery of small amounts of Neanderthal DNA in west African people is most likely to reflect genetic backflow into Africa from Eurasia.

̽��ֱ��consensus view of human history is that the ancestors of present-day humans diverged from the ancestors of extinct Neanderthal and Denisovan groups around 500,000-700,000 years ago, before the emergence of ‘modern’ humans in Africa in the last few hundred thousand years.

Around 50,000-70,000 years ago, some humans expanded out of Africa and soon after mixed with archaic Eurasian groups. After that, populations grew rapidly, with extensive migration and mixture as many groups transitioned from hunter-gatherers to food producers over the last 10,000 years.

̽��ֱ��new data is freely available worldwide to benefit the study of human evolution and genetic diversity, including studies of genetic susceptibility to disease in different parts of the world.

̽��ֱ��team found millions of previously unknown DNA variations that are exclusive to one continental or major geographical region. Though most of these were rare, they included common variations in certain African and Oceanian populations that had not been identified by previous studies – variations that may influence the susceptibility of different populations to disease.

Medical genetics studies have so far predominantly been conducted in populations of European ancestry, meaning that any medical implications that these variants might have are not known. Identifying these novel variants represents a first step towards fully expanding the study of genomics to underrepresented populations.

However, no single DNA variation was found to be present in 100 per cent of genomes from any major geographical region while being absent from all other regions. This finding underlines that the majority of common genetic variation is found across the globe.

“ ̽��ֱ��detail provided by this study allows us to look deeper into human history, particularly inside Africa where less is currently known about the timescale of human evolution,” said Dr Anders Bergström, of the Francis Crick Institute and formerly the Wellcome Sanger Institute. “We find that the ancestors of present-day populations diversified through a gradual and complex process mostly during the last 250,000 years, with large amounts of gene flow between these early lineages. But we also see evidence that small parts of human ancestries trace back to groups that diversified much earlier than this.”

This study was funded by Wellcome and the Francis Crick Institute.

Reference
Bergström, A. et al. Insights into human genetic variation and population history from 929 diverse genomes, Science, March 2020; DOI: 10.1126/science.aay5012

Adapted from a press release by The Wellcome Sanger Institute.

A new study has provided the most comprehensive analysis of human genetic diversity to date, clarifying the genetic relationships between human populations around the world.

It is remarkable that patterns of Neanderthal ancestry are so similar in populations around the world today, and may have derived from a single Neanderthal population.

Aylwyn Scally

Matt Midgley

Handprints in the Cueva de las Manos, Patagonia, made by hunter-gatherers around 9,000 years ago

̽��ֱ��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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Mountain gorilla genome study provides optimism about population numbers

cjb250 — Thu, 09 Apr 2015 18:00:00 +0000

“Mountain gorillas are among the most intensively studied primates in the wild, but this is the first in-depth, whole-genome analysis,” says Dr Chris Tyler-Smith from the Wellcome Trust Sanger Institute. “Three years on from sequencing the gorilla reference genome, we can now compare the genomes of all gorilla populations, including the critically endangered mountain gorilla, and begin to understand their similarities and differences, and the genetic impact of inbreeding.”

̽��ֱ��number of mountain gorillas living in the Virunga volcanic mountain range on the borders of Rwanda, Uganda and the Democratic Republic of Congo plummeted to approximately 253 in 1981 as a result of habitat destruction and hunting. Since then, conservation efforts led by the Rwanda Development Board and conservation organizations such as the Gorilla Doctors, and supported by tourists keen to see the gorillas, have bolstered numbers to approximately 480 among the Virunga population.

Researchers interested to learn how such a small gene pool would affect the mountain gorillas were surprised to find that many harmful genetic variations had been removed from the population through inbreeding, and that mountain gorillas are genetically adapting to surviving in small populations.

“This new understanding of genetic diversity and demographic history among gorilla populations provides us with valuable insight into how apes and humans, their closely related cousins, adapt genetically to living in small populations,” says Dr Aylwyn Scally, from the Department of Genetics at the ̽��ֱ�� of Cambridge. “In these data we can observe the process by which genomes are purged of severely deleterious mutations by a small population size.”

Using blood samples collected over several years by the Rwanda Development Board, ̽��ֱ��Institut Congolese pour la Conservation du Nature and by Gorilla Doctors, which treats wild gorillas injured by snares, researchers were able to sequence the whole genomes of seven mountain gorillas for the first time. Previously, only easily obtainable but poor-quality DNA from faecal and hair samples have been analysed at a handful of regions of the genome.

Scientists discovered that these mountain gorillas, along with eastern lowland gorillas, their closely related neighbours, were two to three times less genetically diverse than gorillas from larger groups in western regions of central Africa. While there are concerns that this low level of genetic diversity may make the mountain gorillas more vulnerable to environmental change and to disease, including cross-infectious strains of human viruses, the inbreeding has, in some ways, been genetically beneficial. Fewer harmful ‘loss-of-function’ variants were found in the mountain gorilla population than in the more numerous western gorilla populations: these variants stop genes from working and can cause serious, often fatal, health conditions.

By analysing the variations in each genome, the researchers also discovered that mountain gorillas have survived in small numbers for thousands of years. Using recently-developed methods, the researchers were able to determine how the size of the population has changed over the past million years. According to their calculations, the average population of mountain gorillas has numbered in the hundreds for many thousands of years; far longer than previously thought.

“We worried that the dramatic decline in the 1980s would be catastrophic for mountain gorillas in the long term, but our genetic analyses suggest that gorillas have been coping with small population sizes for thousands of years,” says Dr Yali Xue from the Sanger Institute. “While comparable levels of inbreeding contributed to the extinction of our relatives the Neanderthals, mountain gorillas may be more resilient. There is no reason why they should not flourish for thousands of years to come.”

It is hoped that the detailed, whole-genome sequence data gathered through this research will aid conservation efforts. Now that a genome-wide map of genetic differences between populations is available, it will be possible to identify the origins of gorillas that have been illegally captured or killed. This will enable more gorillas to be returned to the wild and will make it easier to bring prosecutions against those who poach gorillas for souvenirs and bush meat.

Support for the research came from organisations including the Royal Society, the Wellcome Trust and the National Institutes of Health.

Reference
Xue Y, Prado-Martinez J, Sudmant PH, et al. (2015). Mountain gorilla genomes reveal the impact of long-term population decline and inbreeding. Science. 9 April 2015

An international research project to sequence whole genomes from mountain gorillas has given scientists and conservationists new insight into the impact of population decline on these critically endangered apes. While mountain gorillas are extensively inbred and at risk of extinction, research published today in Science finds more to be optimistic about in their genomes than expected.

This new understanding of genetic diversity and demographic history among gorilla populations provides us with valuable insight into how apes and humans, their closely related cousins, adapt genetically to living in small populations

Aylwyn Scally

Gorilla Doctors

Baby gorilla

̽��ֱ��text in this work is licensed under a Creative Commons Attribution 4.0 International License. For image use please see separate credits above.

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