New insights into evolutionary past uncovered

A new study has provided the most comprehensive analysis of human genetic diversity to date, after the sequencing of 929 human genomes by scientists at the Wellcome Sanger Institute, the University of Cambridge and their collaborators, including Associate Professor Qasim Ayub from the School of Science, Monash University Malaysia.

The study uncovers a large amount of previously undescribed genetic variation. It provides new insights into our evolutionary past, highlighting the complexity of the process through which our ancestors diversified, migrated and mixed throughout the world. The resource, published in Science (20 March), is the most detailed representation of the genetic diversity of worldwide populations to date. It is freely available to all researchers to study human genetic diversity, including studies of genetic susceptibility to disease in different parts of the world.

The consensus view of human history tells us 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 increased, with extensive migration and mixture as many groups transitioned from hunter-gatherers to food producers over the last 10,000 years.

This study 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. The sequencing and analysis of these genomes, which are part of the Human Genome Diversity Project (HGDP)-CEPH panel, now provides unprecedented detail of our genetic history.

Associate Professor Qasim Ayub

The 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 differences in certain African and Oceanian populations that had not been identified by previous studies. Variations such as these may influence the susceptibility of different populations to disease.

However, medical genetics studies have so far predominantly been conducted in people 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.

The study also provides 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. 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.

The discovery of small amounts of Neanderthal DNA in west African people, most likely reflecting later genetic backflow into Africa from Eurasia, further highlights how multiple layers of complexity characterise human genetic history. Until recently, it was thought that only people outside sub-Saharan Africa had Neanderthal DNA.

A former alumnus of the Wellcome Sanger Institute, Associate Professor Qasim Ayub: "When I was collecting some of these samples in the 1990s in Pakistan, I never imagined that sequencing technologies would advance so much that we would be able to generate whole-genome sequences for less than a thousand dollars in a few days. This rich data resource will facilitate genomic studies in under-represented populations".

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