The pioneering work on the human mtDNA tree by Allan Wilson and colleagues (Cann et al. 1987; Vigilant et al. 1991), after some controversy over the methods and the data (reviewed in Forster et al. 2001), quickly focused both geneticists and anthropologists on the probability of a relatively recent African ancestry for all modern humans some two hundred thousand years ago. At most, some geneticists (Templeton 2002; Harding et al. 1997; Green et al. 2010) and anthropologists (Duarte et al. 1999) argue for a possible minor admixture outside Africa of modern Eurasians with already resident hominins such as Homo neanderthalensis or Homo erectus. Supporting evidence for a recent African origin of humans came from Y chromosome research that demonstrated that the two deepest Y branches, now called A and B, are found exclusively in Africans (Underhill et al. 1997).

The establishment of a recent African origin set the scene for the next major discovery in the quest for unravelling human origins – namely, that humans seem to have been restricted to Africa between two hundred thousand years ago and sixty thousand years ago, and only in the last sixty thousand years have successfully ventured out of Africa to settle the rest of the world. This striking paradox was observed in the first large-scale survey of western, eastern and southern Africa by mtDNA analysis conducted by geneticist Elizabeth Watson.

Western Asia, comprising the Arabian Peninsula, the Middle East, Anatolia and parts of the Caucasus, is genetically not obviously related to Central Asia. Briefly, western Asia was the entry point for the small human founder group emigrating from Africa just over fifty thousand years ago, and this group had not yet differentiated into Europeans, Asians or Australians. Today, however, western Asia is inhabited by people resembling, in their physical appearance as well as in their mtDNA and Y types, their European and Caucasian neighbours. To avoid ambiguity, people of European, Caucasian or western Asian descent will be termed “Caucasoid”, in contrast to the “Caucasians” of the Caucasus Mountains. In contrast, Central Asia has a different population history, and a different outcome. Because of the lack of ancient DNA evidence, nothing is known for certain on the initial settlement of Central Asia. We can perhaps extrapolate from ancient DNA recovered in Mongolia more than two thousand years ago, which turns out to be largely European, that Central Asia also must have had a largely European-derived or European-related population until two thousand years ago. This genetic constitution of the Central Asian population must then have changed via East Asian immigration, because Central Asia today has largely East Asian mtDNA and Y types. Thus, if there is any genetic link at all between western and Central Asia, it would be the sharing of a common Caucasoid substrate some time after fifty thousand years ago until becoming admixed more recently, with limited African female genetic input through historic slave trade in the Arabian Peninsula, and a de facto population replacement by East Asian DNA types in Central Asia in the last 2500 years. A small number of key studies have looked at the local history in detail, as follows.

The greatest genetic diversity in East Asians is found in Southeast Asia (Chapter 1.22), and for this reason it is thought that East Asia was first colonised from the south around 50,000 years ago, not long after the exodus from Africa.

Within East Asia, one of the most prominent genetic-geographic features is the north–south difference already noted in classical blood group markers as summarised by Cavalli-Sforza, Menozzi and Piazza (1994) and reproduced in mtDNA data by Forster et al. (2001). The discontinuity is at approximately 45° N latitude, which was also the permafrost boundary during the Last Glacial Maximum twenty thousand years ago. Mitochondrial demographic expansion dates north of this latitude are younger than twenty thousand years, and dates south of this more ancient. This suggests that humans were restricted to southern refuges during the last Ice Age Maximum, and then recolonised the wastelands when the climate improved.

Similar to areas within the northern latitudes, the Tibetan plateau would have represented a significant climatic and environmental challenge to early human settlement. Successful colonisation here requires not only adaptation to the cold, but also adaptation to the hypoxic conditions at more than 3000 metres above sea level. Tibetans today have in fact adapted to the low oxygen levels by virtue of a point mutation in the EPAS1 gene (Yi et al. 2010; Beall et al. 2010). This point mutation influences the production of red blood cells and therefore of haemoglobin in their blood. The polymorphism conferring this advantage shows a 78% frequency difference between Tibetans and Han Chinese, representing one of the fastest human genetic changes to date, assuming Han Chinese and Tibetans separated genetically fairly recently, during the Holocene.

The study of human molecular genetics, made possible through the elucidation of the structure of DNA (Watson & Crick 1953), has in recent years contributed increasingly to the understanding of prehistory. Archaeogenetics, the study of the human past using the techniques of molecular genetics, now provides a framework for investigating the out-of-Africa expansion of our species, Homo sapiens, and the means of elucidating its later population history. It is also informative about the earlier hominin species Homo neanderthalensis.

DNA is the genetic material in all life forms that contains the information determining the form and function of the organism. All organisms, whether humans, fungi or bacteria, consist of cells. These cells are largely constructed of four macromolecular building blocks: proteins, lipids, carbohydrates and the nucleic acids (RNA and DNA). DNA works as the blueprint within each cell for the synthesis of the proteins. The structure of DNA is a double-stranded linear molecule, the so-called double helix. This contains linear sequences of the four chemical bases – adenine, cytosine, guanine and thymine – attached to the DNA backbone. DNA is passed on from one generation to another. In humans, specific cells, egg cells and sperm cells, are the vehicles of transmission.

In animals generally, nuclear DNA and mitochondrial DNA (mtDNA) are distinct entities within each cell, and their mode of inheritance differs. mtDNA is passed down only through the mother to her children. The greater part of the cell’s DNA is packaged into chromosomes that are located in the cell’s nucleus. Here it is necessary to distinguish between the Y chromosome and the other nuclear DNA from the point of view of inheritance. While the Y chromosome is passed down exclusively from father to son, the other nuclear DNA is passed down to the children from both parents.

Introduction

Europe is the only continent where geneticists have analysed substantial numbers of ancient hominins for their DNA, both ancient Homo neanderthalensis and ancient Homo sapiens individuals. The ancient DNA results are partly expected, as in the case of the Neanderthals, but partly contradict previous reconstructions of European prehistory on the basis of modern genetic variation. This may be an omen for other continents, where extensive settlement hypotheses have been proposed on the basis of modern genetic variation, but where ancient DNA has not yet been recovered to the same extent.

The Development of Studies on Modern European DNA

The archaeological record indicates that the first modern humans arrived in Europe via Southeast Europe about forty-five thousand years ago, conventionally associated with the Aurignacian culture. There, modern humans would have encountered Neanderthals, who had existed in Europe for more than two hundred thousand years previously. Neanderthals and moderns lived on the same continent until about thirty thousand years ago, when the Neanderthals suddenly became extinct (the last Neanderthal skeletons are found in southern Spain and Croatia). This extinction may coincide with the appearance of a second modern European culture, the Gravettian, and with a sudden change in the climatic conditions – from erratic climate swings seen during the early Ice Age (sixty thousand to thirty thousand years ago) to much more settled conditions about thirty thousand years ago. Fine-scaled radiocarbon dating reveals that the coexistence of modern humans and Neanderthals at any given location in Europe lasted for less than one thousand years (Mellars 2006). It remains a mystery why the Neanderthals should have succumbed to competition or climate change after inhabiting Europe for so long, but it is possible that the more stable conditions by thirty thousand years ago destroyed any advantages the Neanderthals may have had during the climatically more erratic periods.

Initial Colonisation

Australia was probably occupied by humans at least fifty thousand years ago (Stringer 2002; see Chapter 1.35), at a time when lowered sea levels created a land-bridge between Australia and neighbouring New Guinea, and when the region was separated from the Eurasian landmass by only narrow straits such as are represented by Wallace’s Line. It therefore makes genetic sense to discuss Australia and Highland New Guinea as one unit (Sahul, as it is known), at least as far as the earliest prehistoric colonisation periods are concerned, and to disregard coastal New Guinea, with its Holocene Malayo-Polynesian genetic markers, for the early period.

The dates for the archaeological indications of the first colonisation of Australia are compatible with the out-of-Africa scenario outlined in the introductory chapters and Part II of this book. And the archaeogenetic evidence (which is provided by samples from living Aboriginal populations) gives only limited support for the “multiregional origin hypothesis”. This is important, given the “archaic” appearance of some of the fossil remains – for instance, from Kow Swamp. It should be noted, however, that ancient DNA analyses from early Australian Aboriginal remains have not yet been obtained or published. An adequate synthesis of the archaeogenetic evidence for Australia cannot be achieved until such time as they are.

Modern Native American DNA

Between 1993 and 1996, mitochondrial DNA analyses of Native Americans established the presence of five major mtDNA types A, B, C, D (Torroni et al. 1993a, 1993b) and X (Bandelt et al. 1995; Forster et al. 1996) in the Americas. While types A–D are found across the Americas, X has a regional distribution, being restricted to North America, where it is found approximately along the latitude of the Great Lakes, that is, along the perimeter of the former Laurentide ice sheet. Asians also have these mtDNA types, with A, C and D being widespread and frequent, whereas B is absent in northern Asia, and X is rare or absent throughout Asia.

What is rarely pointed out in this early research, but striking in retrospect, is the very low rate of admixture from European or African females: indeed subjects who report Native American ancestry in their maternal line are almost certain (over 99%) to have one of these five Native American mtDNA types. On the paternal side, as measured by the Y chromosome typing, the story is very different. There are three Native American Y chromosome types, the major type Q, and the rarer types C and O. All of these are found in northern Asia. In addition, and in contrast to the mtDNA picture, there is extensive evidence of European admixture in the male lineages; even in Greenland Eskimos the European Y-chromosomal proportion is found to be as high as 50%. Conversely, in “white” Latin Americans, European Y chromosomes dominate, while Latin American mtDNA is largely or predominantly Native American, along with some African admixture.

Early Settlement

The Indian Subcontinent is the genetically most diverse area in the world outside of Africa, implying an early settlement and maintenance of a relatively large population size not long after the exodus of a small founder group of humans from Africa around fifty thousand years ago (Chaubey et al. 2008). The time taken for this group to migrate from Africa to India and then on to Australia has been estimated genetically at less than fifty-three hundred years (Hudjashov et al. 2007). In a study based on mtDNA analysis, the team of Kivisild and colleagues (Metspalu et al. 2004) describes a package of the three most ancient mtDNA branches, which are specific to and widespread within the Indian Subcontinent: mtDNA branches M2, R5 and U2i. These three branches are between fifty thousand and seventy thousand years old and evidently represent the first successful Anatomically Modern Human settlers on the Indian Subcontinent. The corresponding ancient Indian Y chromosome lineages may include types within the branches C5, H, F, L1 and R2, postulated to be the minimal set to be indigenous to India (Sengupta et al. 2006), which together constitute about a quarter of Indian Y-types.

A possibly different interpretation is offered by Reich and colleagues (2009), who analysed autosomal DNA in twenty-five diverse Indian samples and grouped them phylogenetically by assuming the controversial concept of “fissioning populations”. The concept of population fissions is problematic in cases of long periods where apparently discrete populations of humans can partly or wholly merge at some point in prehistory, confounding the analysis. Bearing this caveat in mind, it is nevertheless interesting that these authors conclude that Indian genetic variation consists of two ancient components, one of which is an “Ancestral South Indian” component whose descendant alleles are found mainly in southern Indians but found in pure form only in the Andaman islanders.

At the beginning of the twentieth century, the countries of the Far East and the Pacific were regarded by the West from the standpoint of imperialism. Economically, they were important to it as sources of raw materials, fields of investment, and markets for manufactured goods. Politically, their relations with Western powers were conducted on terms of inequality. Some countries—especially China—had been compelled to grant the powers concessions in relation to trade and investment and jurisdiction in respect of the latters' nationals residing within their boundaries. Others had become colonies or protectorates. Even Australia, which became a federal Commonwealth in 1901, and New Zealand were not exceptions to the general situation. As high-income countries with predominantly European populations, they occupied advantageous positions within the framework of imperialism; but, though they possessed responsible government, they were subject to British control of their external relations. Japan alone had reached a stage at which the Western powers were beginning to treat her as a full member of the community of nations.

The international standing of Japan had been attained over a remarkably short period. Till the 1850s the country had maintained, for over two hundred years, a policy of seclusion mitigated only by limited contacts with the Chinese and the Dutch. But, within less than fifty years of its enforced entry into treaty relations with the Western powers, it had carried through a programme of political modernisation unequalled elsewhere in Asia. This adaptation to the circumstances of the new age was facilitated by the characteristics of Japanese social and political structure.