Svante Pääbo

1955 - present

Genomes of Extinct Humans

Svante Pääbo is revolutionizing our understanding of human evolution. He is the Director of the Department of Genetics of the Max Planck Institute for Evolutionary Anthropology in Leipzig, Germany.

Our ability to sequence the genome has improved by orders of magnitude since the Human Genome Project completed its first draft in 2003. We have learned amazing things since then about today's humans and many other existing species. By comparing our genome with that of chimpanzees, for example, we can learn not only what really makes us different, but when certain events occurred since we separated from our common ancestor 5.4 million years ago. Analyses such as that done by Katherine Pollard have enabled us to determine exactly what changes in our genome caused this differentiation. By comparing the genomes of different humans from different parts of the world, we can trace the history and timings of migrations that occurred thousands of years ago. Genome databases from humans and many other species are creating research opportunities in every biological field.

However, questions about our exact lineage in terms of other human species in the fossil record cannot be determined solely from examination of the genome of living humans. We need to be able to look at the genomes of extinct human species to do that. That has always seemed to be impossible since the tissues containing DNA are not preserved in fossils...until Svante Pääbo figured out how to do it. It turns out that some DNA is preserved in some teeth and bones of some fossils—but only in minuscule fragmentary amounts. It has taken Pääbo's team years of meticulous process development to be able to extract that DNA, piece it together, and generate the genome of an extinct species. At first this was done only for mitochondrial DNA which is present in higher volume but later was accomplished for the more important nuclear DNA. One of the big problems facing everyone attempting to accomplish this is that in the process of performing the laboratory analyses, contamination of DNA from the researchers and/or fossil handlers has confused the analysis. Microscopic particles from human skin or airborne saliva or other sources can easily contaminate the fossil specimens. This could have occurred anywhere in the handling of the fossils including even at the site at which they were originally discovered. The Pääbo team has developed the methods to detect and eliminate such contamination and has created special "clean" laboratories for these analyses.

So far, the complete genomes of two extinct human species has been determined: Neanderthals and Denisovans. In fact, this genome analysis from the few teeth and bone fragments we have available, is the only way we even know that Denisovans existed and were a species distinct from other humans.

What we have learned from these analyses is amazing! First of all, the DNA from current Europeans contains 1-2% of their DNA from Neanderthals. A similar amount of Neanderthal DNA is contained is today’s Asians. However, no Neanderthal DNA is contained in today’s Africans. Wow!!! That means that Neanderthals did not emerge until the predecessor to modern Homo sapiens had already left Africa. Neanderthals had separated from an earlier hominin, probably Homo heidelbergensis, at least 500,000 years ago. Since that was before modern Homo sapiens appeared, the Neanderthals are not in our direct ancestral line. The genome analysis confirms that there was a small amount of interbreeding between Neanderthals and Homo sapiens that must have occurred after “Out of Africa 2.” That is, the Neanderthals split from a more ancient human species that left Africa at an earlier time (Out of Africa 1). Then, since Homo sapiens emerged later in Africa, it was after the Homo sapiens migration from Africa (Out of Africa 2) that the interbreeding occurred. Since Neanderthal DNA shows up in Europeans and Asians about the same amount, it suggests that the interbreeding could have occurred in the Middle East before Homo sapiens spread in the two directions. Similarly, some of today’s Asians and particularly those in Oceania contain as much as 3-6% of their DNA from Denisovans whereas Europeans contain no Denisovan DNA. Native Americans do have Denisovan DNA. This pattern would confirm that Homo sapiens interbred with Denisovans to a small extent while they were on their way to North American through Asia.  Neanderthal DNA is 99.7% identical to Homo sapiens DNA. That’s a lot closer than we are to chimps.

Some of the evidence we’re getting from extinct genomes is making things muddier. Svante Pääbo’s group have recently been able to painstakingly extract enough mitochoncrial DNA from some ancient bones in Spain to cast doubt on the date Homo sapiens diverged from its predecessor. The DNA confirmed that these ancient fossils were Neanderthals. But the striking thing about this is that their age is much older than previously thought indicating that the date that Homo sapiens may have split from our predecessor may be as early as 700,000 years ago rather than 200,000 years ago. This depends on which version of our lineage turns out to be correct. Several alternatives are discussed in the book. The more we are able to tease out DNA from ancient fossils and compare them to a growing database of DNA from living humans around the world, the more complicated our history seems to get. There probably were at least five distinct periods and locations where interbreeding occurred between Homo sapiens and ancient—now extinct—human species.

Hopefully, Pääbo's team will soon be able to extract the DNA for other extinct human species and either further illuminate or further complicate our history.

Click on links to other players in my journey below.