Out of Africa: more data must give us definite answers, soon ….

Mr. Aubrey Lynch, elder from the Wongatha Aboriginal language group, who participated in the study

Mr. Aubrey Lynch, elder from the Wongatha Aboriginal language group, who participated in the study. Credit: Preben Hjort, Magus Film

DATE: 26/09/16
By Yali Xue

On 21st September, three papers presenting genome sequences from diverse humans went online in Nature, with much subsequent coverage in the scientific and general press. How did it feel to be involved in them?

Working in a genomic institute in a team called ‘Human Evolution’, I naturally want genomic data from people from all over the world to investigate our evolutionary history. A few years ago, the 1000 Genomes Project started, providing for the first time whole genome sequences from all over the world. This was my dream, exactly what I wanted, and would surely allow us to answer all our questions! It was certainly a great project, yet ……. the sequences were not completely accurate (low coverage), and more importantly, some key populations were missing.

The basics of human evolutionary history are clear: we evolved in Africa. But now people are present all over the world. Surprisingly, the some of the earliest evidence for human presence outside Africa is found on the other side of the world, in Australia. Understanding this early migration by studying their living descendants should help us understand how humans changed from being an endangered African species to a worldwide one that endangers every other species.

I wished and dreamed to have an accurate dataset (high-coverage) from Aboriginal Australians and as many other worldwide populations as possible. With that we would surely be able to answer all our questions, including one of biggest and most debated ones in the field: one exit or two exits from Africa 60,000 years ago or earlier?

Now we have that dataset; even beyond my dreams, we have three, all of which I was privileged to be involved in, and all published this week in the same issue of Nature. Three dedicated international teams worked for years with sample donors and got them interested, sequenced their DNAs (the easy bit) and them sweated for ages analysing the sequences. So what was the answer?

All three studies agree that there was one main exit. But the word “main” is crucial here. One study talks about one exit, one says there was at least a 2% contribution in some populations from a second exit, and the third allows both of these possibilities. Despite such rich datasets, involvement of almost all the top scientists in the field, and the best available analytic methods, we cannot agree 100% on this question.

Human history is complicated, and we are trying to use modern population data to infer human history 60,000 years ago. So 787 high-quality DNA sequences from key populations are great, but ……. now I dream of ancient DNA sequences from 60,000 years ago and many years on either side, from all over the world. With those, we will surely be able to answer this question and lots of others …….

In China, we say that if you are satisfied with what you have, you will be happy. We are really happy with what we have achieved now, but in science, we would always like to be happier.

So I have to keep dreaming …

Yali Xue is a senior staff scientist in the Human Evolution group at The Wellcome Trust Sanger Institute. Her initial interest was in using variation on the Y chromosome to provide insights into aspects of human history and evolution. Now her work has extended to study patterns of variation throughout the entire human genome and to reveal further evolutionary insights, including medically-relevant ones.

Publications

Anna-Sapfo Malaspinas et al. (2016) A genomic history of Aboriginal Australia. Nature. DOI: 10.1038/nature18299 

Swapan Mallick et al. (2016) The Simons Genome Diversity Project: 300 genomes from 142 diverse populations. Nature. DOI: 10.1038/nature18964

Luca Pagani et al. (2016) Environmental challenges  and complex migration events during the peopling of Eurasia. Nature. DOI: 10.1038/nature19792

Further links:

Human evolution group at the Sanger Institute: http://www.sanger.ac.uk/science/groups/tyler-smith-group

The genetic history of Aboriginal Australians and Papuans: http://www.sanger.ac.uk/news/view/genetic-history-aboriginal-australians-and-papuans