Ancient DNA
A genetic perspective on human origins
Matthew Williams and |
Who are we? Where did we come from? Why are we here? These fundamental questions have been |
João Teixeira (University |
widespread throughout human history, shared across dierent cultures from distant epochs and |
of Adelaide, Australia) |
geographical locations. The search has been as much a philosophical as an empirical one, capturing |
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the imagination of the philosopher, the theologian, the artist and the scientist alike. Hence, the quest |
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for unveiling our origins is probably as old as humanity itself. From a scientic point of view, which |
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we address in the present article, the question of human origins became deeply intertwined with |
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Charles Darwin’s theory of evolution in the late 19th century. This led to the development of scientic |
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elds such as palaeoanthropology, which analyses fossil remains, stone tools and cultural artefacts |
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to piece together our past. Recently, however, the possibility to assess genetic information from |
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thousands of individuals across the world and, more importantly, to obtain DNA from specimens that |
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lived thousands of years in the past |
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genomes have to tell us about where we came from. Ultimately, however, can they tell us who we are? |
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Within most scientic disciplines a complex relationship exists between Occam’s razor, which states that the simplest explanation is best, and Bonini’s paradox, elegantly put by the philosopher and poet Paul Valéry: ‘Everything simple is false. Everything complex is unusable’. This is particularly true for aDNA research. As researchers, we are not simply trying to infer oen immeasurably complex demographic events from relatively small amounts of incomplete data, but likewise historical events. us, to understand the history of our species, aDNA studies rely on synthesizing population genetics theory and modelling with archaeological and palaeoanthropological fossil record reconstructions.
Of necessity, the genetic models are oen overtly simple caricatures of human demography and do not fully capture the complexity of human societal structure through time. erefore, it is the duty of the researcher, and the broader scientic community, to understand how violations of these models impact the interpretation of genetic results. Moreover, it is of growing importance to eectively communicate that, whilst we reconstruct the past using simplistic genetic models, these models should not be interpreted simplistically.
Models of human evolution
e prevailing view amongst palaeoanthropologists well into the
followed prevailing racial theories about human populations. Hence, this period was dominated by an evolutionary polygenist view of human origins, which asserted, at the time, that geographically dispersed human populations had separately evolved from dierent species at dierent evolutionary times. However, when the concept of human races lost its scientic validity during the second half of the 20th century, evolutionary polygenism was abandoned as a valid scientific hypothesis and replaced by two contrasting (and competing) models of human evolution: multiregional evolution and Out of Africa. e development of these two models has historically been associated with the analysis and interpretation of the fossil record, with a particular focus on geographical variation and continuity (or lack thereof) of morphological traits through time.
Multiregional evolution states that geographical variation observed in the fossil record starting in the early Pleistocene should be interpreted as intraspecic diversity existing within the genus Homo, which denes the human species. e theory builds strongly upon Franz Weidenreich’s model of an intricate network of human evolution across a wide geographical area spanning the Old World. Multiregionalism maintains that while most of the human population lived in Africa throughout the Pleistocene, there was a continuous (in time and space) network of gene ow between human populations that lived in relative isolation from one another. is process allowed a relative, but never complete, isolation of human groups in dierent parts of the Old World,
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Ancient DNA
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Human admixture |
90,000 years ago |
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into Neanderthals |
‘Ghost’ admixture |
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EUROPE |
100,000 years ago |
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into Denisovan |
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Denisova Cave |
EAST ASIA |
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Unknown ‘Archaic’ |
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admixture into humans |
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~50,000 |
years ago |
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Unknown ‘Archaic’ |
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admixture into humans |
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U |
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D |
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SOUTH ASIA |
~50,000 years ago |
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Human range |
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AFRICA |
Neanderthal range |
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Denisovan range
NNeanderthal admixture into humans
AUSTRALIA
D Denisovan admixture into humans
UUnknown admixture into humans
Possible human route out of Africa
Figure 1. Human evolution during the late Pleistocene. Before human populations migrated out of Africa and into dierent parts of the world, Eurasia was occupied by several ‘archaic’ human groups, such as Neanderthals in the West (blue) and Denisovans in the East (red). Genetic studies have shown that an early group of humans moved out of Africa ~100,000 years ago and admixed with Neanderthals; Denisovans and Neanderthals met and interbred in Siberia ~90,000 years ago; an unknown divergent group admixed with Denisovans, probably in East Asia/Siberia. These events are depicted by pink arrows and occurred before the migration of human populations out of Africa
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whereby humans were a polytypic species. e process of gene ow mediated by continuous migrations across the landscape, mostly from Africa to dierent parts of Eurasia in a process named
In sharp contrast, the Out of Africa theory considers that the human species, Homo sapiens, emerged ~250,000 years ago somewhere in eastern/southern Africa, much more recently than proposed by multiregional evolution. A key stance/position of the Out of Africa model is that features of modernity rst arose in Africa around this time and then spread around the rest of the world
years ago through a major expansion of anatomically modern humans into Eurasia. e expansion of modern humans across the planet resulted in the replacement of existing
Population genetics and personal ancestry
e debates regarding modern human origins in the light of these two competing models coincided with the growing availability of genetic information across populations around the world. e advantage of using DNA to trace the history of our species through time is that we know, since the rediscovery of the work of
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Ancient DNA
Gregor Mendel, how genetic information is transmitted from parents to offspring. More importantly, we can also estimate the mutation rate of DNA, i.e., how many errors occur on average in the copying of DNA in each generation. Hence, by contrasting the number of dierences between any two DNA copies we can estimate the time to the most recent common ancestor between them.
The first genetic studies tackling the question of human origins made use of mitochondrial DNA (mtDNA), a small fragment of DNA that is present in mitochondria, cellular organelles that function as energy powerhouses for each of the cells in our body. As there are thousands of mitochondria in each cell, mtDNA is highly abundant and easy to obtain. Importantly, each of us inherits mtDNA through our mother, whereby mtDNA is a direct source to unveil the history of our maternal ancestry. In a highly impactful article, published in 1987, Cann, Stoneking and Wilson demonstrated that all the mtDNA diversity found in contemporary human populations emerged from a single mtDNA lineage that arose in Africa ~200,000 years ago. This finding strongly supports the Out of Africa theory, and even an extreme variation of the model, known as Eve theory, as an allusion to Biblical accounts of creation. Importantly, because mtDNA is transmitted only through the maternal side, it contains no information regarding the paternal ancestry of human populations. However, there is another genetic marker, the
Nonetheless, things get more complicated, as both mtDNA and the
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fraction of genetic ancestry in each individual human. If we consider only two generations in the past, neither of these markers oers any information on the maternal grandfather nor the paternal grandmother of a given individual and, as a consequence, of none of their ancestors. In fact, the further back we go in time, the more genetic ancestral information we fail to include from our own family tree, at an exponential rate.
So, how do we assess the genetic information passed on for millennia from our vast family tree? e answer is in the nucleus of the cell. As readers of e Biochemist will be aware, humans have 22 pairs of autosomal chromosomes, one of each inherited from each of our parents, plus the sex chromosomes. is nuclear genome contains the overwhelming majority of genes that encode most of the biological functions in our body, from growth to metabolism and immunity. Due to the cut and paste nature of recombination during gametogenesis, this genetic information is inherited from our entire family tree in a
aDNA and our extended family tree
So, what does the information contained in our nuclear genome say about the origin of our species? e analyses of genomic data across contemporary human populations around the world conrms that the majority of our genetic ancestry traces back to Africa. Importantly, populations currently living outside of Africa are the descendants of a migration of people from Africa
However, a recent revolution in the field of evolutionary biology, beginning in the 21st century, has made it possible to obtain DNA sequences from ancient remains and established the field of aDNA. e availability of ancient genomes has allowed us to uncover previously hidden chapters in the history of our species, namely remarkable population migrations and admixture events. In a groundbreaking article published in 2010, Svante Pääbo and colleagues sequenced the rst complete Neanderthal genome. To the astonishment of many palaeoanthropologists, by comparing the
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Ancient DNA
Neanderthal genome to those of contemporary human populations, Pääbo and colleagues showed that Neanderthals had contributed ~2% to the genetic ancestry of
Population genetics and personal ancestry
Advancements in genetics research have revolutionized our conceptions of the history of our species; introducing us to unknown groups such as the Denisovans and
revealing the place of Neanderthals in our family tree. Thus, we can expect that genetic research, coupled with the palaeo and archaeo sciences, will take us far in answering the second of the three questions we posed at the beginning of this article – ‘where did we come from?’ However, the question of human origins is as much personal as it is academic, and answering the remaining two questions: ‘who are we?’ and ‘why are we here?’ – will require more than robust statistical models about human demography. In a time where over 26 million
As discussed above, the process of recombination shues up chromosomes. Individuals have two copies of each autosomal chromosome but only pass on a single mixed copy to their progeny, leaving one of the homologous genomic regions behind. As a consequence, for each generation in your family tree, the amount of genetic information you inherit from that particular ancestor is halved. In other words, the further back you go the less genetic information any given ancestor directly contributed to you. is brings us to the somewhat surprising fact that there are genealogical ancestors in your family tree who are not your genetic ancestors. You only have to go back on average nine generations to nd direct biological ancestors from whom you have inherited no genetic information, as it was lost in the lottery of genetic assortment before it could make it to you.
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Ancient DNA
Alongside this rather paradoxical concept is an equally obscure thought. During the 1st century BCE it is estimated that the global population numbered approximately 300 million people. If we take a generation time of 25 years, there are 80 or so generations between the present day and the 1st century BCE. If we then assume that for someone living today their ancestors were all unique individual people extending back to the 1st century BCE, they would have 1.2 ⋅ 1024 ancestors; notably that is 4 ⋅ 1015 more ancestors than there were people alive at that time. is
Further reading
geographically, has led to surprising results suggesting that the most recent genealogical ancestor of all present- day humans lived only a few thousand years ago. Further work by Ralph and Coop in 2013 looking at
So, on these seemingly contradictory paradoxes; the exponential increase in the number of ancestors with the simultaneous reduction in genetic contribution by any single ancestor, emerges one of the most powerful and unifying propositions of population genetics, that “no matter the languages we speak or the colour of our skin, we share (genealogical) ancestors who planted rice on the banks of the Yangtze, who rst domesticated horses on the steppes of the Ukraine, who hunted giant sloths in the forests of North and South America, and who laboured to build the Great Pyramid of Khufu” (Rohde, Olson and Chang, 2004). ■
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•Wolpo, M.H., Wu, X. and Thorne, A.G. (1984) Modern Homo sapiens origins: a general theory of hominid evolution
involving the fossil evidence from East Asia. In: The Origins of Modern Humans: A Worm Survey of the Fossil Evidence (Smith, F.H. and Spencer, F. eds) pp.
•Cann, R.L., Stoneking, M. and Wilson, A.C. (1987) Mitochondrial DNA and human evolution. Nature 325,
•Stringer, C.B. and Andrews, P. (1988) Genetic and fossil evidence for the origin of modern humans. Science 239,
•Green R.E., Krause, J., Briggs, A.W. et al. (2010) A draft sequence of the Neanderthal genome. Science 328,
•Reich, D., Green, R.E., Kircher, M. et al. (2010) Genetic history of an archaic hominin group from Denisova Cave in Siberia. Nature 468,
•Ralph, P. and Coop, G. (2013) The geography of recent genetic ancestry across Europe. PLOS Biology 11, e1001555
•Graham Coop blog GCbias https://gcbias.org/ (Accessed 26/11/19)
•MIT Technology Review Report:
•Rohde, D.L.T., Olson, S. and Chang, J.T. (2004) Modelling the recent common ancestry of all living humans. Nature 431,
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Matthew P. Williams is an archaeogenetics PhD candidate at the Australian Centre for Ancient DNA, University of Adelaide. Matthew obtained a bachelor’s degree in Ancient Near Eastern History from Macquarie University, Sydney, and his
master’s in gical Science from the Australian National University, Canberra. Matthew’s doctoral research focuses on reconstructing the demographic history of ancient Near Eastern and indigenous Australian populations by synthesizing historiographical and archaeological research with population genetic models and ancient DNA. Email: matthew.williams01@ adelaide.edu.au
João C. Teixeira is a population geneticist based at the Australian Centre for Ancient DNA at the University of Adelaide. Before moving to Australia, João obtained his PhD in Evolutionary Genetics at the Max Planck Institute for Evolutionary Anthropology,
in Leipzig, Germany, supervised by Dr Aida Andrés and Professor Svante Pääbo. João’s research combines population genetics and comparative genomics to understand how demography and natural selection inuence the evolution of human populations and closely related species. João is particularly interested in Pleistocene human evolution, human population adaptation to environmental change and historical human migrations in Europe. Email: joao.teixeira@adelaide.edu.au
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