University of Huddersfield Repository Soares, Pedro, Rito, Teresa, Pereira, Luísa and Richards, Martin B. A Genetic Perspective on African Prehistory Original Citation Soares, Pedro, Rito, Teresa, Pereira, Luísa and Richards, Martin B. (2016) A Genetic Perspective on African Prehistory. In: Africa from MIS 6-2. Vertebrate Paleobiology and Paleoanthropology, IV . Springer, London, UK, pp. 383-405. ISBN 978-94-017-7519-9 This version is available at http://eprints.hud.ac.uk/id/eprint/27955/ The University Repository is a digital collection of the research output of the University, available on Open Access. Copyright and Moral Rights for the items on this site are retained by the individual author and/or other copyright owners. Users may access full items free of charge; copies of full text items generally can be reproduced, displayed or performed and given to third parties in any format or medium for personal research or study, educational or not-for-profit purposes without prior permission or charge, provided: • The authors, title and full bibliographic details is credited in any copy; • A hyperlink and/or URL is included for the original metadata page; and • The content is not changed in any way. For more information, including our policy and submission procedure, please contact the Repository Team at: [email protected]. http://eprints.hud.ac.uk/ Sacha C. Jones and Brian A. Stewart (eds.), Africa from MIS 6-2: There is a consensus across the fields of genetics, Population Dynamics and Paleoenvironments, Vertebrate archaeology and palaeoanthropology that Africa is Paleobiology and Paleoanthropology, DOI 10.1007/978-94-017- 7520-5_18 the cradle of Homo sapiens. Genetically, across the genome-wide autosomal variation and the uniparental markers, the mitochondrial DNA (mtDNA) A genetic perspective on African prehistory and Y-chromosome, Africa is the continent with by far the highest genetic diversity (Torroni et al. 2006; Behar et al. 2008; Li et al. 2008; Cruciani et al. 2011). Pedro Soares1, Teresa Rito1, Luísa Pereira1,2, Martin B. 3 However, with a few exceptions, this is where the Richards 1 consensus ends. A whole range of crucial questions IPATIMUP (Instituto de Patologia e Imunologia Molecular remain highly controversial. These include: where in da Universidade do Porto), Porto, Portugal Africa modern humans first appeared; when each 2 Faculdade de Medicina da Universidade do Porto, Porto, part of Africa was first colonized by modern humans; Portugal the impact of climate change on human populations; 3 School of Applied Sciences, University of Huddersfield, and how cultural and technological innovations Queensgate, Huddersfield HD1 3DH, UK helped shape the current genetic diversity in the African continent. Correspondence should be addressed to: Martin Richards ([email protected]) Genetics can contribute valuable insights into the origins and migrations of human populations. The Keywords: rationale for this lies in the fact that mutations and climate change recombination, the events promoting changes in the migration molecular clock genome down the generations, are random mtDNA phenomena that leave marker buoys scattered phylogeography throughout the genome, each of which arose at a population expansions particular time and place. They can therefore serve as an inference tool to bracket the place and timing of Running title: Genetic perspective on African prehistory evolutionary events. The relatively small, maternally inherited mtDNA Abstract component (around 16,570 base pairs) has been The various genetic systems (mitochondrial DNA, the heavily screened worldwide, initially for short Y chromosome and the genome-wide autosomes) segments of the fast-evolving, non-coding control- indicate that Africa is the most genetically diverse region (>150,000 samples), and more recently for the continent in the world and the most likely place of whole-mtDNA genome. By 2013, more than 15,000 origin for anatomically modern humans. However, whole-mtDNA genome sequences have become where in Africa modern human arose and how the publicly available, including more than 2000 from current genetic makeup within the continent was African individuals. Whole-mtDNA genomes, in shaped is still open to debate. Here, we summarise particular, can resolve the details of the maternal the debate and focus especially on the maternally- genealogy in exquisite detail. An even greater level of inherited mitochondrial DNA (mtDNA) and a recently genealogical resolution awaits us for the male line of revised chronology for the African mtDNA tree. We descent, inscribed in the non-recombining, male- discuss the possible origin of modern humans in specific part of the Y chromosome, or “MSY”, as southern, eastern or central Africa; the possibility of a human genome sequencing proceeds apace. migration from southern to eastern Africa more than Although some analyses have suggested drastic 100 ka, carrying lineages within mtDNA haplogroup reductions on the number of MSY lineages in the L0; the evidence for a climate-change-mediated recent past due to the reproductive success of population expansion in eastern Africa involving relatively few individuals, it may also be the case that mtDNA haplogroup L3, leading to the “out-of-Africa” the MSY often tracks important dispersals, leading to migration around 70–60 ka; the re-population of the spread of language families, that are much less North Africa from the Near East around 40–30 ka evident from the mtDNA variation (Forster and suggested by mtDNA haplogroups U6 and M1; the Renfrew 2011). In the end, models erected using evidence for population expansions and dispersals either the mtDNA or the MSY have to be tested across the continent in the onset of the Holocene; and against variation in the rest of the genome. The the impact of the Bantu dispersals in central, eastern analysis of genome-wide autosomal markers, and and southern Africa within the last few millennia. increasingly complete human genomes, provides a more complete window onto the past that does not focus on one or other single line of descent. 1 Nevertheless, mtDNA led the way for archaeogenetics with difficulties. Moreover, we are increasingly and remains an extremely valuable marker system. learning that these issues do not go away when The mtDNA, like the MSY, is non-recombining, leading ancient DNA comes into play – although this is not for to the transmission down the generations of the the present an issue so far as Africa is concerned. genetic material in a block – essentially, a single DNA On the other hand, the critics sometimes fail to sequence. As it is passed down the generations acknowledge both the extraordinary richness of the mutations accumulate, leading to the formation of genetic evidence – whether it be the extraordinarily related clusters called haplogroups, each of which can fine resolving power of mtDNA or MSY phylogenies, trace its descent back to a single common ancestor. A or the incredible autosomal profiling that is now haplogroup is effectively a named example of what possible – or the successes that phylogeographic evolutionary biologists call a clade – a group reconstructions have achieved in cases where the comprising an ancestor and all its descendants. Any demographic history is broadly known from other ancestral node in the genealogical tree can, lines of evidence – such as the settlement of the moreover, be dated using the “molecular clock” – a Americas, the Remote Pacific, and indeed southern measure of how rapidly mutations accumulate over Africa, as we discuss below. Rather than a hard-line time – an approach that remains controversial, but set of protocols in which demographic history is read which has seen considerable progress recently in all from scratch from DNA sequence data using three systems, with the use of whole mtDNA statistical tools of dubious reliability, we prefer an genomes (Soares et al. 2009), the autosomes with the exploratory and interdisciplinary approach in which development of large-scale complete human genome hypotheses are evaluated within the framework of sequencing (Scally and Durbin 2012) and the MSY as models supplied by archaeology, palaeoanthropology, much larger genomic tracts of the Y chromosome palaeoclimatology and so on. start to be used (Wei et al. 2012; Francalacci et al. 2013). Thus, if a migration takes place from one In this chapter we focus primarily on the patterns in region to another, new mutations unique to that the mtDNA variation and review the main respects in region will start to accumulate there, and the age of which the phylogeographic analysis of this particular the presence of that cluster in that region can be molecule can provide information about the history estimated by dating the node from which they arise. of the continent, in the context of some of the This tracking of genetic lineages (or lines of descent) autosomal and MSY work. For a broader view of the in time and space by analyzing their geographic mtDNA variation we can recommend the recent distribution and time depth is referred to as review by Rosa and Brehm (2011). “phylogeography”, and the dating of dispersals in this way in particular is called “founder analysis”. The The maternal genealogy of Africa resolving power of the mtDNA genealogical tree makes mtDNA an extremely powerful tool with which The African mtDNA tree is effectively the human to evaluate population structure and follow mtDNA tree, since the deepest two-thirds of the migrations across space and time (Torroni et al. 2006; lineages are restricted to Africa, and the non-African Macaulay and Richards 2013). lineages are only a tiny fragment of African diversity. Any phylogenetic tree comprises nodes separated by Phylogeographic approaches have been criticised on branches, in a nested array of clades and subclades – a range of fronts, and have often been compared clusters of lineages that include all descendants of a unfavourably to both more formal and supposedly given common ancestor (a subclade is simply a clade robust procedures such as those based on simulation within a clade).