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A Genetic Perspective on Human Origins

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A Genetic Perspective on Human Origins 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 Downloaded from http://portlandpress.com/biochemist/article-pdf/42/1/6/867100/bio042010006.pdf by guest on 03 October 2021 of Adelaide, Australia) geographical locations. The search has been as much a philosophical as an empirical one, capturing the imagination of the philosopher, the theologian, the artist and the scientist alike. Hence, the quest for unveiling our origins is probably as old as humanity itself. From a scientic point of view, which we address in the present article, the question of human origins became deeply intertwined with Charles Darwin’s theory of evolution in the late 19th century. This led to the development of scientic elds such as palaeoanthropology, which analyses fossil remains, stone tools and cultural artefacts to piece together our past. Recently, however, the possibility to assess genetic information from thousands of individuals across the world and, more importantly, to obtain DNA from specimens that lived thousands of years in the past (so-called ancient DNA [aDNA] analyses) is rapidly transforming long-held beliefs about our origins. As such, we have never been in a better position to ask what do our genomes have to tell us about where we came from. Ultimately, however, can they tell us who we are? Within most scientic disciplines a complex relationship followed prevailing racial theories about human exists between Occam’s razor, which states that the populations. Hence, this period was dominated by an simplest explanation is best, and Bonini’s paradox, evolutionary polygenist view of human origins, which elegantly put by the philosopher and poet Paul Valéry: asserted, at the time, that geographically dispersed ‘Everything simple is false. Everything complex is human populations had separately evolved from dierent unusable’. This is particularly true for aDNA research. species at dierent evolutionary times. However, when As researchers, we are not simply trying to infer oen the concept of human races lost its scientic validity immeasurably complex demographic events from during the second half of the 20th century, evolutionary relatively small amounts of incomplete data, but likewise polygenism was abandoned as a valid scientific historical events. us, to understand the history of our hypothesis and replaced by two contrasting (and species, aDNA studies rely on synthesizing population competing) models of human evolution: multiregional genetics theory and modelling with archaeological and evolution and Out of Africa. e development of these two palaeoanthropological fossil record reconstructions. models has historically been associated with the analysis Of necessity, the genetic models are oen overtly and interpretation of the fossil record, with a particular simple caricatures of human demography and do not focus on geographical variation and continuity (or lack fully capture the complexity of human societal structure thereof) of morphological traits through time. through time. erefore, it is the duty of the researcher, Multiregional evolution states that geographical and the broader scientic community, to understand variation observed in the fossil record starting in the how violations of these models impact the interpretation early Pleistocene should be interpreted as intraspecic of genetic results. Moreover, it is of growing importance diversity existing within the genus Homo, which denes to eectively communicate that, whilst we reconstruct the human species. e theory builds strongly upon Franz the past using simplistic genetic models, these models Weidenreich’s model of an intricate network of human should not be interpreted simplistically. evolution across a wide geographical area spanning the Old World. Multiregionalism maintains that while most Models of human evolution of the human population lived in Africa throughout the Pleistocene, there was a continuous (in time and space) e prevailing view amongst palaeoanthropologists well network of gene ow between human populations into the mid-20th century was dominated by an that lived in relative isolation from one another. is imperialistic interpretation of the fossil record, whereby process allowed a relative, but never complete, isolation phylogenetic classications of human fossil variation of human groups in dierent parts of the Old World, 6 February 2020 © The Authors. Published by Portland Press Limited under the Creative Commons Attribution License 4.0 (CC BY-NC-ND) Ancient DNA Neanderthal-Denisovan admixture 90,000 years ago Human admixture into Neanderthals 100,000 years ago ‘Ghost’ admixture EUROPE into Denisovan Denisova Cave EAST ASIA 60-50,000 years ago Unknown ‘Archaic’ Downloaded from http://portlandpress.com/biochemist/article-pdf/42/1/6/867100/bio042010006.pdf by guest on 03 October 2021 N admixture into humans D ~50,000 U years ago Unknown ‘Archaic’ admixture into humans U D SOUTH ASIA ~50,000 years ago Human range D AFRICA Neanderthal range Denisovan range N Neanderthal admixture into humans AUSTRALIA D Denisovan admixture into humans U Unknown admixture into humans Pre-out of Africa admixture events 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 ~60–50,000 years ago. The potential routes taken by migrating human populations are shown in black arrows and should be interpreted cautiously, as they remain speculative. Before leaving Africa, human populations probably admixed with an unknown ‘archaic’ human population (purple U circle). Further admixture events occurred soon after humans left Africa: with Neanderthals ~60–50,000 years ago in the Middle East (blue N circle); with another ‘archaic’ group in South Asia (purple U circle); and with Denisovans in East Asia, Island Southeast Asia and the Philippines ~50,000 years ago (red D circles). whereby humans were a polytypic species. e process years ago through a major expansion of anatomically of gene ow mediated by continuous migrations across modern humans into Eurasia. e expansion of modern the landscape, mostly from Africa to dierent parts of humans across the planet resulted in the replacement of Eurasia in a process named centre-and-edge, promoted existing (so-called) archaic forms in Eurasia, such as the the spread and xation of advantageous traits across Neanderthals of Europe. the entire network, whereby no geographical place for modernity can be easily ascribed. Population genetics and personal ancestry In sharp contrast, the Out of Africa theory considers that the human species, Homo sapiens, emerged ~250,000 e debates regarding modern human origins in the years ago somewhere in eastern/southern Africa, much light of these two competing models coincided with more recently than proposed by multiregional evolution. the growing availability of genetic information across A key stance/position of the Out of Africa model is that populations around the world. e advantage of using features of modernity rst arose in Africa around this time DNA to trace the history of our species through time and then spread around the rest of the world ~60–50,000 is that we know, since the rediscovery of the work of February 2020 © The Authors. Published by Portland Press Limited under the Creative Commons Attribution License 4.0 (CC BY-NC-ND) 7 Ancient DNA Gregor Mendel, how genetic information is transmitted fraction of genetic ancestry in each individual human. from parents to offspring. More importantly, we can If we consider only two generations in the past, neither also estimate the mutation rate of DNA, i.e., how of these markers oers any information on the maternal many errors occur on average in the copying of DNA grandfather nor the paternal grandmother of a given in each generation. Hence, by contrasting the number individual and, as a consequence, of none of their of dierences between any two DNA copies we can ancestors. In fact, the further back we go in time, the estimate the time to the most recent common ancestor more genetic ancestral information we fail to include between them. from our own family tree, at an exponential rate. The first genetic studies tackling the question So, how do we assess the genetic information passed of human origins made use of mitochondrial DNA on for millennia from our vast family tree? e answer (mtDNA), a small fragment of DNA that is present in is in the nucleus of the cell. As readers of e Biochemist mitochondria, cellular organelles that function as energy will be aware, humans have 22 pairs of autosomal Downloaded from http://portlandpress.com/biochemist/article-pdf/42/1/6/867100/bio042010006.pdf by guest on 03 October 2021 powerhouses for each of the cells in our body. As there chromosomes, one of each inherited
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