Introduction: DNA two hundred thousand years ago, and left from there to colonise the world, with little if any admixture with resident hominin groups or species such as Neanderthals or Homo erectus. The long-term effective population size of the human lineage since the human–chimpanzee split roughly 6 million years ago has been calculated to be of the order of ten thousand persons. This value is based on uncertain demographic assumptions such as generation times and may in itself not be meaningful, but it is significantly smaller than the estimated population size at other points in the primate evolutionary tree (Takahata & Satta 1997). Significantly smaller again, the group leaving Africa possibly sixty thousand years ago (Watson et al. 1997; Forster et al. 2001) may have numbered less than a few hundred (Macaulay et al. 2005; Forster 2009). This initial small founding population size outside Africa explains why non-Africans are fairly similar to each other genetically, whereas the diversity among Africans tends to be greater. In the fossil record, the exodus of this small group of humans from Africa around sixty thousand years ago has not (yet) been identified. Instead, older human remains in the sites of Skhul and Qafzeh (Israel/Palestine) dated to around 90,000 to 130,000 years (Stringer 2007) demonstrate that an earlier exodus from Africa happened but was ultimately unsuccessful in settling the world. These hominins are assigned to an archaic form of the species Homo sapiens and it is believed they have no successors. DNA has not been recovered from them. The robustness of these fossils (e.g., prominent brow ridges) is outside the morphological range of modern humans, supporting the genetic evidence that the Skhul/Qafzeh remains were probably an evolutionary dead-end. Their findspot may have been at the limit of an internal African expansion that populated Africa more than eighty thousand years ago (Watson et al. 1997). Also, there is a theoretical possibility that these robust modern humans contributed DNA to the modern Eurasian population to a very limited extent, if certain autosomal DNA variants typical for Eurasia are considered to be ancient there (Templeton 2002; Green et al. 2010). Following this line of thought, it is relevant that the earliest known modern European cranium, dated to forty thousand years ago and from Peştera cu Oase, Romania (Trinkaus et al. 2003), is thought by some to have archaic features (Roberts 2009). Alternatively, it can be argued that all Eurasian-specific autosomal variants are descended from the African exodus of sixty thousand years ago, with the African counterparts dying out since then, whereby any robust or archaic morphological features in modern Eurasians, Australians and Americans have redeveloped by chance.
Ancient DNA Archaeogeneticists are typically interested in tracing the prehistoric ancestry of living individuals; they seek, for example, to find out about the ancestors’ arrival times in various parts of the world, or to find out when they developed specific features such as depigmented skin, milk digestion in adulthood or malaria resistance. To achieve this, it is necessary to analyse the
DNA of living individuals rather than of prehistoric fossils, as there is no guarantee that any particular prehistoric fossil contributed genes to the present population. However, analysing the DNA of fossil remains, along with ancillary organisms such as human parasites and domesticated plant and animal species, is important to reconstruct the context in which our ancestors lived. Specifically, a fossil hominin DNA profile can tell the researcher when that fossil’s lineage split from our lineage and allows speculation as to how different genetically that hominin would have been from our human ancestors. Even datasets derived from modern DNA generally contain numerous errors (reviewed in Dennis 2003; Forster 2003), and it is therefore no surprise that errors are also a significant feature of ancient DNA datasets. Similarly, first attempts to obtain whole-genome data from ancient Neanderthal DNA have had to be retracted due to contamination problems, identified by J. D. Wall and S. K. Kim (2007). Ideally, ancient DNA data should be validated, and this can be achieved in a number of ways. For example, archaeogeneticists can type the DNA of known descendants of the ancient DNA sample (as in the case of the descendants of Marie Antoinette; see Jehaes et al. 2001). Another approach is the typing of accompanying animal bones to prove that the environmental conditions permitted ancient DNA survival. Another is the typing of several prehistoric human individuals from the same context, in the expectation that they would systematically differ in their DNA from any modern DNA. Initial ancient DNA studies in the 1980s and 1990s were met with scepticism, coming to a head when successful retrieval of 80 million–year-old dinosaur DNA had been claimed and then shown to be modern DNA contamination (Zischler et al. 1995). The first mtDNA sequence obtained from a Neanderthal was the first convincing and significant breakthrough in ancient DNA analysis (Krings et al. 1997) and incidentally did not require any of these controls, as the resulting sequence was on the one hand clearly nonhuman, but on the other hand retained some ancient mtDNA variants predicted in some of the deepest African mtDNA branches of modern humans (Watson et al. 1997). The Neanderthal sequence by Krings and his colleagues, obtained from the Feldhofer type fossil in the Neander Valley in western Germany, was soon validated by independent analyses of other Neanderthals (Ovchinnikov et al. 2000), and showed that humans and Neanderthals had split approximately half a million years ago. This new timescale led to the popularisation of the proposal that Homo neanderthalensis was related through an ancestral African Homo heidelbergensis to modern humans (Lahr & Foley 1998). Another important advance that came about through ancient DNA studies of Neanderthals is a better appreciation of their geographic range. Fossil bones in central Asia that hitherto were too fragmentary for species assignment were shown, by ancient DNA analysis, to be Neanderthal, thus expanding the known range of Neanderthals eastwards by at least 2000 km (Krause et al. 2007). The picture might appear more complicated, however, with the ancient DNA analysis of another fossil fragment from the Caucasus Mountains, which reveals that the hominin in question is neither human 15