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The Archaeogenetics Research Group

Schematic global phylogenetic tree of human mtDNA haplogroups, showing the subclades of the main non-African clades M and N coalescing to the African L lineages about 70 ka and to the human most recent common ancestor about 190 ka.

A new chronology for the human mtDNA tree. Branch lengths were estimated using maximum likelihood and the time-dependent molecular clock. Ages are expressed in kya. (See Soares et al. 2009) Click the image to view at full size.

Archaeogenetics tells the story of the spread of humanity around the world, from our roots hundreds of thousands of years ago in Africa to the movements of people within the last few hundred years. This work encompasses everything from the route that early humans took out of Africa when they settled the rest of the world, to the spread of farming in Africa, Asia and Europe, the peopling of the Pacific Islands and the Jewish diaspora.

The Archaeogenetics Research Group studies the geographic distribution of modern human genetic variation, with the aim of addressing questions from archaeology, anthropology and history. We do this primarily by combining the phylogenetic relationships between the lineages with their geographic distribution and diversity converted to time depth using the molecular clock, an approach termed ‘phylogeography’. Our main target until recently has been mitochondrial DNA (mtDNA), which is inherited without recombination down the female line of descent, allowing us to make inferences from estimates of the human maternal genealogy. We are increasingly also applying the phylogeographic approach to Y-chromosome variation, which traces the male line of descent, and studying genome-wide variation in the autosomes. Our work involves active collaboration between ourselves and archaeologists, such as Prof Douglas Baird (Liverpool), Dr David Bulbeck (ANU, Australia), Dr William Davies and Prof Clive Gamble (Southampton), Prof Sir Paul Mellars (Cambridge/Edinburgh) and Prof Mohd Mokhtar Saidin and Dr Stephen Chia (USM, Malaysia), exemplifying the group’s philosophy of a harmonious marriage between archaeology and genetics.

We focus on several of what the archaeologist Clive Gamble has called the “big questions” of archaeology – the origins of modern humans, the global colonisation of the world by the human species, and the origins and spread of agriculture. These global or continental-level questions are the kind that can be addressed by phylogeographic approaches to contemporary genetic data, by looking at the spread of genetic lineages across time and space, in work carried out in our Archaeogenetics Laboratory. Increasingly, though, a more fine-grained approach is becoming possible with the advent of ancient DNA methods, and by using our new Ancient DNA Facility we hope to be able to not only test models erected on the basis of modern variation but also to address smaller-scale changes in prehistory such as events at the end of the Neolithic and in the medieval period. The facility includes a level 7 clean-room suite, for the analysis of historical and prehistoric remains, and was designed specifically for dealing with human samples – the most challenging kind of ancient DNA research, due to the pervasive problems with contamination. Both labs are managed by Dr Maria Pala.

Our interest range widely, but our primary areas of research have been (1) the origins of modern humans in Africa and their dispersal into the rest of the world, (2) the settlement of Europe, and (3) the settlement of Southeast Asia and the colonisation of the Pacific. At the same time, especially in collaboration with our colleague Professor Hans-Jürgen Bandelt at the University of Hamburg, we have pursued new analytical approaches suited to the data we are using and the questions we want to ask. Our work has featured in many TV documentaries such as the BBC Two series The Incredible Human Journey and BBC One’s Andrew Marr’s History of the World and Meet the Izzards, and provides the science behind much of the genetic ancestry testing industry.

African origins and the colonisation of the world

Following our earlier work outlining the maternal genetic history of Africa with Dr Antonio Salas of the University of Santiago de Compostela in Galicia, Spain, we proposed a model for the dispersal of modern humans out of Africa that has been widely accepted. In research published in 2005 in the journal Science, funded by the Royal Society and the Discovery Channel, and carried out in collaboration with colleagues including statistician Dr Vincent Macaulay of Glasgow University, Prof Antonio Torroni of Pavia University in Italy and the author Prof Stephen Oppenheimer of Oxford University, we focused on the process of the initial dispersal of modern humans out of Africa and the peopling of the world. We argued that modern humans dispersed primarily along the “southern coastal route” along the coastlines of the Red Sea and the India Ocean and on into Southeast Asia and Australasia. With funding from the Bradshaw Foundation, the Portuguese FCT and the Leverhulme Trust, we have continued to the details of the dispersal process, including the possible role of the eruption of the super-volcano Toba about 75,000 years ago, which we argue predated the dispersal, and – in collaboration with Dr Luisa Pereira at IPATIMUP in Porto and Dr Pedro Soares of the University of Minho, Braga, in Portugal – the possible role of the “Gulf oasis” as a glacial refuge from which Eurasian may have dispersed to the rest of the world after their arrival from Africa around 55,000 years ago.

You can read about the Leverhulme award in the Trust’s newsletter (April 2012, p.8):

More recent research is described in this University news article and on Eurekalert 

Who are the Europeans?

Our longest-running research programme is our work on the prehistoric settlement of Europe. Europe was first settled by modern humans about 45,000 years ago, but there has been a long-standing debate about the extent to which Europe was resettled when agriculture arrived from the Near East with the Neolithic, around 9000 years ago. This remains an active area of research as ancient DNA contributes more and more to the discussion. Our earlier work with mtDNA suggested that the majority of Europeans are descended from lineages that arose during expansions of hunter-gatherers from glacial refuge areas in southwest Europe at the end of the Ice Age, with only a minority arriving from the Near East with the Neolithic. With a particular focus on the Near East, especially Anatolia, we have now been aiming to further test our earlier conclusions using the greater resolving power of whole-mtDNA sequences, in work funded by the Leverhulme Trust (carried out by Dr Martin Carr) and Portugal’s FCT (carried out by research students shared with IPATIMUP), and in collaboration with Prof Torroni, Dr Macaulay and Dr Pereira and Dr Soares. In fact, our more recent work led by Dr Maria Pala, and in collaboration with Prof Torroni, has pointed to expansions from a Near Eastern refuge at the end of the Ice Age too.

University news article reporting this project

Schematic phylogenetic tree of human mtDNA haplogroups commonly seen in Europeans, Southwest Asians and North Africans, showing the main subclades N1, X, R0, JT and U, some of which have a deep ancestry in Europe (up to almost 50 ka) and some of which arrived from the Near East more recently.

Schematic phylogenetic tree of human mtDNA haplogroups in Europe, Southwest Asia and North Africa. The timescale is based on ML estimates and a time-dependent complete mtDNA genome clock. Haplogroups colour-coded according to their region of origin. (See Soares et al. 2010) Click the image to view full size

Researchers are increasingly turning to ancient DNA to resolve these issues, and we hope that work in our new Ancient DNA Facility will contribute to this debate, as well as many others. We were involved with one of the earliest whole-mtDNA genomes to be sequenced from an ancient human, that of the Tyrolean Iceman.

This is part of a recent body of ancient DNA research showing that central Europe was settled by incoming farmer communities in the early Neolithic, 7500 years ago – a community that later declined, leaving little signal in the modern populations. This kind of discovery can only be made by looking at ancient remains. With his work at the Australian Centre for Ancient DNA and subsequently at Huddersfield, Dr Paul Brotherton, has also contributed enormously to this date with his work on ancient DNA from early central European farmers.

The settlement of Southeast Asis and the Pacific Islands

Another significant avenue of research in the past few years, funded by the British Academy, the Bradshaw Foundation and the Portuguese FCT, has been the prehistory of Southeast Asia and the Pacific islands. In order to do this we had first to re-calibrate the mutation rate of the mtDNA molecular clock, and correct for the effects of natural selection, in a project led by our colleague Dr Soares when he was a member of the group.  (Calculator available here.) Dr Soares, now in Braga, continues to collaborate closely with our group.

Our findings have again challenged the consensus view of archaeologists and linguists concerning the history of the region, in which expanding farming communities from South China and Taiwan play the major role. They support the suggestion of our colleague, the author Dr Stephen Oppenheimer, that sea-level changes at the end of the last Ice Age were the main driving force behind dispersals and settlement in this part of the world, and suggest that the main source for the settlement of Polynesia was in the New Guinea region, rather than China/Taiwan. We are continuing to extend this work with further studies of both island and mainland Southeast Asia, in close collaboration with Dr Soares and Dr Pereira and a shared FCT PhD student, Dr Andreia Brandão, and with a Libyan Government-funded PhD student, Tarek Shoeib.

New York Times  and Science Newsline coverage

Most recently, in collaboration with Dr Pereira and Dr Soares, we have explored the maternal ancestry of Ashkenazi Jews, with the controversial finding that the majority of their mitochondrial lineages trace back to prehistoric Europe rather than the Near East. This suggests that they descend on the female side from converts within Europe, rather than from first-century migrants from Palestine.

Coverage from Science Magazine, New York Times, The Scientist, Genetic Literacy Project, BBC News

Last updated Friday 11 December 2015
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