Palaeogenomics

Palaeogenomics is revolutionising our understanding of human evolution and who we are. Oxford University Professor of Archaeological Science Tom Higham explains what palaeogenomics is and some of the exciting findings coming from this field.

Transcript

PROF TOM HIGHAM

Genetics has really blown this field apart, and palaeogenomics is a really exciting area of research. So everyone is familiar with DNA testing. Hardly a week goes by where there’s some evidence for DNA testing coming to the rescue of the legal profession, of the police in finding murderers, and this is revolving of course around modern DNA. But palaeo DNA, ancient DNA, is a completely different field and one in which it’s much, much more challenging, because of course rather like with the collagen, the amount of DNA in a bone slowly starts to degrade and disappear over time until eventually there’s nothing left. In certain parts of the globe, in warmer environments, DNA really doesn’t survive at all. It’s only in the colder parts, the more temperate locations, that you get a lot of DNA. But with modern techniques, even the more difficult locations and older locations are starting to yield genetic data that can be relied upon.

So there are two main types of DNA that we can use in ancient DNA research. They come from two different parts of the cell. One is the mitochondrial part of the cell, which is mitochondrial DNA, which are matrilineally inherited, so they come down from the mother to mother to mother, all the way through. On the other side of the coin in the nucleus is the nuclear DNA, which is diploid inherited, coming from both parents.

This is Svante Pääbo – he’s a colleague of ours from the Max Planck in Leipzig – and he has been at the forefront of ancient genetics work in the Palaeolithic ancient DNA, particularly of Neanderthals, and in 2005, his team and a group of other researchers stated that they were going to attempt to sequence the Neanderthal genome. And this very ambitious project was built around developments in instrumentation, which we call next-generation sequencing. Without going into too much of the detail, basically what this means is that you take small sections of the DNA and you can knit them together using a fantastic machine which allows you to build up lots and lots of small pieces of DNA and compare them to genomes of modern humans that we all, of course, already have.

So Svante and his team were looking for bone which had suitable DNA preservation, and they eventually found three bones from the site at Vindija Cave in Croatia, and these three bones furnished almost all of the Neanderthal genome DNA data. In the end, in 2010, when they published this paper – A Draft Sequence of the Neanderthal Genome – they’d sequenced around 55% of the Neanderthal genome. Whereas previously we had no evidence and no information from the mitochondrial DNA that there was any interbreeding or any interaction between modern humans and Neanderthals, the genome completely changed the interpretation, and it showed clearly that we had interbred with Neanderthals. And it also allowed us to put a figure on the amount of DNA that we share, and that figure is between 1.5 to 2.1%.

Outside of Africa, all non-Africans share a very similar amount of this DNA from Neanderthals. So if you’re an Australian Aborigine or a person in France or a person in China, India, whatever, you have almost exactly the same amount. So this means that the movement of the ancestral populations of these modern humans must have happened after the interbreeding event with Neanderthals took place.

The Science Learning Hub would like to acknowledge: Professor Tom Higham, University of Oxford The Allan Wilson Centre for Molecular Ecology and Evolution Footage of laboratory and re-enactment footage of ancient modern humans, courtesy of Max Planck Institute for Evolutionary Anthropology Photos of Johannes Krause, Adrian Briggs, Ed Green and Svante Pääbo with a Neanderthal skeleton reconstruction and fragments of three Neanderthal bones from Vindija Cave, courtesy of Max Planck Institute for Evolutionary Anthropology Schematic of nuclear and mitochondrial DNA, University of California Museum of Paleontology’s Understanding Evolution Image of Svante Pääbo with thigh bone courtesy of © MPI for Evolutionary Anthropology/Bence Viola Photos of Pääbo’s Neanderthal research group, clean lab at MPI, DNA clusters on Roche 454 Genome Analyzer, Frank Vinken, Max Planck Institute for Evolutionary Anthropology Photo of entrance of Vindija Cave, Croatia, Johannes Krause, Max Planck Institute for Evolutionary Anthropology Academic paper image, A Draft Sequence of the Neanderthal Genome, Richard E Green, Johannes Krause, Adrian W Briggs, Tomislav Maricic, Udo Stenzel, Martin Kircher, Nick Patterson, Heng Li, Weiwei Zhai, Markus Hsi-Yang Fritz, Nancy F Hansen, Eric Y Durand, Anna-Sapfo Malaspinas, Jeffrey D Jensen, Tomas Marques-Bonet, Can Alkan, Kay Prüfer, Matthias Meyer, Hernán A Burbano, Jeffrey M Good, Rigo Schultz, Ayinuer Aximu-Petri, Anne Butthof, Barbara Höber, Barbara Höffner, Madlen Siegemund, Antje Weihmann, Chad Nusbaum, Eric S Lander, Carsten Russ, Nathaniel Novod, Jason Affourtit, Michael Egholm, Christine Verna, Pavao Rudan, Dejana Brajkovic, Željko Kucan, Ivan Gušic, Vladimir B Doronichev, Liubov V Golovanova, Carles Lalueza-Fox, Marco de la Rasilla, Javier Fortea, Antonio Rosas, Ralf W Schmitz, Philip L F Johnson, Evan E Eichler, Daniel Falush, Ewan Birney, James C Mullikin, Montgomery Slatkin, Rasmus Nielsen, Janet Kelso, Michael Lachmann, David Reich, Svante Pääbo. Science, 07 May 2010: 710-722