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Edition 60

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Essay

Owning the science

The power of partnerships

SCIENCE AND RESEARCH has an important role to play in the fundamental debate Australians are now having about the rights of this country’s First Peoples and their recognition. This manifests in many ways, but one example powerfully illustrates it. A widespread concern for many Indigenous communities centres on difficulties regarding the repatriation of ancient remains and the connections with kin for members of the stolen generations. Genomic science can bring knowledge and know-how to help address these complex issues, by developing new methods and working in partnership with Indigenous communities and individuals. This research has resulted in new methods to improve recovery of DNA from ancient remains and improved sequencing of complete genomes of living people. This produces new knowledge and, when done collaboratively, results in ownership of the research and its findings by Indigenous people. Ten years after Kevin Rudd’s Apology to Australia’s Indigenous peoples, this research is timely and may help to repair some of the damages of the past.

Aboriginal Australians occupy a unique place in human history worldwide and their biological ancestry is one of the most important in the history of human origins. Although genetic studies have revealed a great deal about human origins in many other parts of the world, until recently relatively little was formally known about Aboriginal Australians. This mainstream neglect is for two general reasons. First, early ancient DNA studies focused on attempts to recover genomic sequences from remains locked in permafrost conditions, or at least from mild temperate environments. This is because degradation of DNA is reduced in low temperatures, and there was widespread belief that DNA would not have survived in the hot environments characteristic of much of Australia. Second, in relation to contemporary DNA research, there have been valid concerns among many of Australia’s First People as some researchers acted unethically in DNA-based research with the Indigenous people, providing little consultation or control over who would use the samples, or clarity about the purpose of the research. Scientists need to work in a robust partnership with Indigenous communities to repair this relationship.

Mungo Man is the oldest known Australian, at about forty-two thousand years, and has long been a central figure in attempts to understand of the origins of Australia’s First Peoples. His return to country, together with the remains of more than a hundred ancient people from the Willandra Lakes region in far-west New South Wales on 17 November 2017, brought into focus the prospect of returning ancient people to their communities. For many decades, remains of the Willandra Lakes people were held in storerooms in universities and museums in Canberra and Sydney.

Previous studies have focused on understanding Mungo Man’s physical remains. But, more recently, new methods to analyse ancient DNA have been developed to recover his genetic material and that of other ancient First People. These new technologies, together with methods to sequence the entire genetic constitution of large numbers of people living today, are directly able to help Indigenous communities with issues of social concern to them. For example, as this article will explain, these developments provide important information regarding repatriation of ancient remains from museums and other institutions around the world and potentially the reconnection of members of the stolen generations to their kin.

 

THE RESEARCH CONDUCTED by my group at the Australian Research Centre for Human Evolution, looking at ancient and modern genomes of Aboriginal Australians, was born out of a desire not simply to recover DNA sequences from ancient remains, but also to help form a bridge between Indigenous and scientific knowledge about the history of people on this continent.

Scientific and Indigenous knowledge systems have often been in conflict. In my view, too much is made of these conflicts: they have a lot in common. For example, Indigenous knowledge typically takes the form of a narrative, usually a spoken story about how the world came to be. In a similar way, evolutionary theories, which aim to explain why particular characters are adapted to certain functions, also take the form of narratives. Both narratives are mostly focused on ‘origins’.

From a strictly genetic perspective, progress on origins research in Australia has been particularly slow. Early ancient DNA studies were focused on remains from permafrost conditions in Antarctica and cool temperate environments such as northern Europe, including Greenland. But Australia is very different. Here, human remains are very old, and many are recovered from very hot environments.

While ancient DNA studies have played an important role in informing understanding of the evolution of our species worldwide, little is known about the levels of ancient genomic variation in Australia’s First Peoples – although some progress has been made in recent years. This includes the landmark recovery of genomic sequences from both contemporary and ancient Aboriginal Australian remains.

Mungo Man and Mungo Lady have been the subject of both Indigenous and scientific narratives. From a scientific perspective, in 1968 the burnt remains of a woman were recovered at Lake Mungo by Jim Bowler, a young geologist. Six years later, after heavy rain, Bowler was riding his motorbike around the lake and again found human remains, this time of a man.

From an Indigenous perspective, it was not that Jim Bowler discovered these ancient people but that they found him. And of course, one is struck by the apparent coincidence that they both revealed themselves to the same person, albeit six years apart. Professor Jim Bowler is a distinguished scientist who has close ties with, and an understanding of, Australia’s First Peoples, so Mungo Lady and Mungo Man chose well.

Perhaps the most well-known conflict between scientific and Indigenous perspectives relates to the origins of Aboriginal Australians. From an Indigenous perspective, Aboriginal Australians have always been on this land – since the Dreamtime. From a scientific perspective, there is strong evidence that they have been here for more than sixty-five thousand years – not quite ‘always’. From my perspective, though, sixty-five thousand years seems pretty close to ‘always’, and, moreover, it is likely that people became Aboriginal Australians when they first set foot on this land. So, in this sense, they have indeed always been here.

 

AMONG THE DELUGE of scientific discoveries that fill our daily news, only a few topics regularly attract the attention of readers worldwide. One is the origin and evolution of our species. All individuals, societies and cultures are fascinated by human history. Recent scientific studies of this subject have focused on where modern humans evolved and how they dispersed across the globe. Australia and its First Peoples have been at the centre of these studies, but largely as objects of study, not as leaders and designers of this research.

Years ago, as a professor of evolutionary biology, I regularly received books on human evolution in my mailbox. These textbooks were of limited interest to me at the time because they typically described fossilised remains. Such remains are mineralised and do not contain living material. Even today, the study of fossils remains outside the scope of most current molecular methods. Instead, I was more interested in sub-fossils, the bones that still retain DNA and proteins, and can therefore be studied using a range of molecular tools such as DNA sequencing. Since the turn of this century, there has been a series of quite remarkable advances in relation to our capacity to recover DNA from sub-fossil remains. These have surpassed all expectations. I now take an especially keen interest in new discoveries in human evolution as they are reported, because they have the potential to trace origins at the level of DNA sequences.

The improbable science of making sense of ancient DNA formally began in the 1980s with the work of New Zealander Allan Wilson. In 1984, Wilson and his co-workers reported the cloning into a bacterial vector and the subsequent sequencing of a short fragment of DNA from the tissue of an extinct quagga, a type of zebra, taken from a museum hide. Later the development of the polymerase chain reaction (PCR), a powerful DNA amplification method, enabled the direct recovery of targeted DNA sequences from humans and a wide range of animals, plants and microbes.

The development of PCR was plagued by scepticism. Many suggested it would not be possible to recover any significant amounts of ancient DNA using this method, let alone an entire genome. For a start, the sequences that can be recovered by PCR are short – and DNA is a very long molecule. It contains more than three billion base pairs, and if you were to stretch out the DNA from just one cell in your body it would be about two metres long. If you were inclined to stretch out all the DNA from all the cells in your body, it would be about twice the diameter of the solar system in length. To recover such extraordinary lengths of DNA using short-targeted regions seemed highly improbable.

And the story gets worse. When you die, your long DNA gets ‘eaten up’ by enzymes called ‘nucleases’, and by the huge populations of bacteria and viruses in your body. So rather like Humpty Dumpty falling off the wall, your DNA molecules are quickly broken into very short pieces. Ancient DNA studies show that these sequences can be as short as fifty or sixty base pairs in length, which is a miniscule proportion – 0.0000017 per cent – of the genome itself.

As it turned out, this damage actually helped scientists to recover complete ancient genomes. The pattern of damage was in fact a signal of authenticity that made it possible to distinguish genuine ancient sequences from contamination from other sources (bacteria or viruses, for example). The challenge then was to put Humpty Dumpty back together. How would it be possible to recover, for example, a human genome of more than three billion base pairs from the myriad of very short DNA sequences? In a remarkable twist of fate, the development of a new generation of DNA sequencers requires long DNA molecules to be deliberately cut into short pieces, in order for the technology to work. As ancient DNA is already sheared into short lengths, this new technology was ideal for its recovery.

In combination, all these developments resulted in the improbable science of ancient DNA becoming probable, and the recovery of large tracts of ancient DNA – even whole genomes – became a reality, suggesting that concerns DNA would not survive in the hot environments characteristic of much of Australia might be misplaced.

When a publication by Professor Alan Thorne, a prominent Australian anthropologist, and his colleagues from the Australian National University appeared in the Proceedings of the National Academy of Sciences of the United States of America in 2001, it drew worldwide attention. The authors reported the recovery of short mitochondrial DNA from Mungo Man, as well as the other ancient remains of a number of people from the Willandra Lakes region. The results from their analysis, which included an evolutionary tree of recovered DNA sequences, suggested that Mungo Man was genetically different to the other ancient people they studied, who were closely related to the Aboriginal Australians of today. This implied that contemporary Aboriginal Australians replaced another population of humans that lived here first.

This conclusion caused widespread offence among Aboriginal people, though it was difficult for them to reject the scientific claims. Some scientists argued that Thorne’s results were highly unlikely to be correct, given the age of the remains and the hot environment in which they had been interred. It was not, however, possible to refute these claims without a detailed understanding of the methods used and the opportunity to redo the experiment. Some politicians and commentators seized on the result to argue against constitutional recognition of Aboriginal Australians, suggesting there was considerable doubt about their First Peoples status.

 

BIG PERSONALITIES HAVE dominated Australian archaeology and anthropology, and influenced its development – Alan Thorne prominent among them. He first became involved in the Lake Mungo excavations under the archaeologist Jim Bowler in 1969, reconstructing the remains of the skeleton of Mungo Lady. Five years later he also reconstructed Mungo Man and led excavations at other important burial grounds in Victoria. Thorne was very well known for his work on the multiregional evolution hypothesis, a model of human evolution that disputed the more widely known recent African origin (or ‘out of Africa’) hypothesis.

For more than a decade after Thorne’s research was published in 2002, his work on Mungo Man and other ancient people from Willandra went largely unchallenged, despite the distress it caused to Aboriginal Australians. Then, in 2010, with the permission of the Paakantji, Ngyiampaa and the Mutthi Mutthi peoples of the Willandra Lakes, my colleagues and I from the Australian Research Centre for Human Evolution were able to resample these important remains. With the advantages of technology that had developed in the preceding decade, we repeated much of the original work. The new technology meant that we were able to recover much smaller amounts of DNA (if it was still present in the remains) and sequence it.

In 2016, we also published the results in the Proceedings of the National Academy of Sciences of the United States of America. Our findings provided strong evidence to refute the claims made by Thorne and his colleagues, showing it was not possible to recover any DNA that unequivocally belonged to Mungo Man. We did, however, recover five distinct DNA sequences from his remains. But these sequences revealed no ancient DNA damage patterns, indicating that they were not ancient sequences – and genetic analysis showed that they were European in origin. Clearly these were sequences from people who left their DNA on the bone material after handling Mungo Man’s remains.

Our study set the record straight. We refuted the claim that Mungo Man was a member of an earlier group of people that previously inhabited Australia and not an Aboriginal Australian. Perhaps of equal importance, we were able to recover substantial coverage of the mitochondrial genome from another ancient Willandra Lakes man, who was buried only a few hundred metres from Mungo Man. The remains contained about 1 per cent human DNA; from them, we were able to recover two complete mitochondrial genomes. One of these was a previously unidentified Aboriginal Australian mitochondrial genetic type, almost certainly from the remains themselves. The other was European in origin, and certainly a contaminant.

It appeared that this man was from within the Holocene period; we know this because the skeletal remains were not heavily mineralised. His teeth exhibited a pattern of wear typical of Aboriginal hunter-gatherer populations and included no evidence of cavities or tooth decay. Combined with the lack of mineralisation in the bone and its position in the soil layers at Lake Mungo, various authors have suggested that the remains were a few thousand years old. This is important, because it means that he represents the best ‘proxy’ currently available for Mungo Man.

The fact that he was buried so close to the oldest-known Australian, albeit much later, suggests a common place and country. This is particularly significant given that the environmental conditions were very different at the times of the two burials, which were about forty thousand years apart. Hence, nuclear gene studies of this man, currently underway, will be especially relevant to our understanding of Mungo Man himself. And because the nuclear genome is much larger than the mitochondrial, it will reveal much more information. Such nuclear genome studies enable us to establish kinship relationships between people living now and ancient peoples. Such studies will take substantial time and effort, and will require the development of new innovative genomic tools. Ethical considerations demand Aboriginal involvement in both the design and operation of such new techniques, as well as new research relationships with Indigenous communities.

 

BIG PERSONALITIES BEGET big ideas. Although scientific information suggests that Aboriginal Australians are the descendants of the first major migration out of Africa, this has not always been the scientific view and is also not a view held by many Aboriginal people.

Earlier, South-East Asia was considered by some as the possible centre of origin of contemporary humans. The earliest example of this view was proposed in 1891 by the Dutch paleoanthropologist and geologist Eugène Dubois, who played an important role in early scientific understanding of human evolution in this part of the world. Dubois was stimulated by the writings of Alfred Russel Wallace, the naturalist and co-discoverer of natural selection, who intuitively linked the presence of gibbons and orangutans in Sumatra and Borneo to the evolution of humans, following Ernst Haeckel’s suggestion of the hypothetical human ancestor Pithecanthropus (from the Greek pithekos meaning ‘ape’ and anthropos meaning ‘man’). Dubois, convinced about the relationship between gibbons and orangutans and humans, enlisted as a doctor in the Royal Netherlands East Indies Army and travelled to Sumatra in search of the ‘ancient man’. Dubois discovered specimens in Java that would have profound implications for scientific understanding of human evolution. Named Pithecanthropus erectus (later redesignated Homo erectus or ‘Java Man’), these were the first specimens of early hominid remains found outside of Africa or Europe.

Just as Dubois dominated the early scientific considerations of human evolution in South-East Asia, Alan Thorne’s influence is writ large across the landscape of formal scientific ideas about human evolution in Australia. Many of Thorne’s ideas are rooted in the worldview of Dubois, whose focus on the robust skeletal features of Homo erectus led Thorne to suggest that Aboriginal Australians might have a South-East Asian origin.

The current scientific view is that Australia’s First Peoples have remained largely isolated since their arrival on this continent. Until recent developments in the study of genomes, the dating of skeletal remains and craniometrics were the only methods to investigate the age and geographic origin of Aboriginal Australians. Although the time of first human arrival is still debated, a paper published in Nature in 2017 by Chris Clarkson and his team from the University of Queensland presents strong evidence for human occupation of the continent as early as sixty-five thousand years ago. This is based on the presence of a wide variety of distinctive stone tool assemblages, including grinding stones, ground ochre and hatchet heads, at a site in Arnhem Land.

The understanding of the timing of many events in human history continues to be revised. In January 2018, research from Mathieu Duval and Rainer Grün from the Australian Research Centre for Human Evolution dated a newly discovered human fossil from the Misliya Cave in Israel at 177,000–194,000 years old. This introduces a new perspective into our view on modern human dispersal and is consistent with recent genetic studies, which have posited the possibility of an earlier dispersal of Homo sapiens out of Africa around 220,000 years ago.

 

BY ASSESSING LEVELS of genetic variation, molecular methods provide a different approach to determining when and where people entered the Australian continent. Molecular clock and statistical models provide us with possible dates, while population differentiation informs us about the number and location of settlements.

Until quite recently, there was very little known about genomic variation in the First Peoples of Australia, although some research had been published on mitochondrial DNA variation. The results of mitochondrial DNA studies are however, of limited help; using them to estimate the time of arrival of Homo sapiens on the Australian continent isn’t precise. Instead, population genetic modelling of nuclear data is required to assess the timing of such events. For this reason, we reported a large number of whole genomes of Aboriginal Australians in 2016. We showed that Aboriginal Australians and Papuan people are mostly the descendants of a single group of people who travelled to this part of the world around fifty-eight thousand years ago, and that Aboriginal Australians and Papuans are more closely related to each other than they are to any other group of people worldwide. Papuans are the closest kin of Aboriginal people. From this study, we also showed that Papuans and Aboriginal Australians separated from each other around thirty-seven thousand years ago, long before the formation of the Torres Strait sea barrier some ten thousand years ago.

Aboriginal Australian groups started to differentiate approximately thirty-one thousand years ago. This was probably a result of the formation of the central deserts during the last great ice age, which would have acted as a barrier to the movement of people. We showed that Aboriginal Australians living in south-western Australia are genetically quite different to those in the north-east. Importantly, we also found a relationship that suggested the Pama-Nyungan languages evolved with the genomes of the people who speak them. The only difference was that our genetic analyses showed that the Pama-Nyungan people evolved these differences over a relatively long period of time, whereas the languages have been thought to have evolved only recently. This raises new and important questions for
future research.

The number of complete genomes mapped of Aboriginal Australians is currently eighty-three. As the approach our research used becomes more powerful and refined, a much finer-scale genomic map of Aboriginal Australia will emerge. Unequivocally, the evidence shows that Aboriginal Australians were the first humans to live on this continent and that they have been here continuously for at least sixty thousand years. A recent study of the eighty-three complete genomes detected a genetic bottleneck in the ancestral Australo-Papuan population about fifty thousand years ago, which overlaps with archaeological evidence for the earliest occupation of both Sunda (Malay archipelago, Sumatra, Java, Borneo and Sulawesi) and Sahul (New Guinea, the Australian continent and Tasmania) between forty-seven and fifty-five thousand years ago. This overlap supports the idea that this is the date of at least one settlement of South-East Asia.

Aboriginal Australians had a complex society in Australia before people ever reached Europe. Research has demonstrated that, using nuclear genomes of Aboriginal Australians living today, we have the technical ability and genetic knowledge to repatriate ancient remains to their original place and country. This is an issue of longstanding concern to First Peoples in Australia and one of relevance to Indigenous peoples worldwide. A similar approach now makes feasible the reunification of members of the stolen generations with their original families. Regarding the former, there is strong support from almost all quarters. In relation to the latter, the question now is not so much can this be done, but should it be done? What are the political, legal and social implications for these community members, and what do they want?

 

IN THE PAST, some scientists have disregarded the rights and views of Aboriginal Australians. This was clearly evident when researchers demanded samples with little or no explanation about their purpose – as was the case with the Human Genome Diversity Project. Led by Professor Cavalli-Sforza from Stanford University in the 1990s, this was an international research project that attempted to sample tissue from six hundred Indigenous communities around the world, including Australia. The researchers took blood and hair samples from many Aboriginal Australian communities, with little consultation or control over who would use the samples and for what purpose after they had been collected. One community group dubbed it the ‘Vampire Project’. This program ultimately had its funding withdrawn, but not before reinforcing Indigenous distrust of Western science and scientific methods.

Overcoming the legacy of distrust requires scientists to recognise the ethical responsibilities of their research. Some still maintain an implicit belief that scientists have the right to freely access samples and genetic material from any Indigenous group for their own use. Others frighten Aboriginal people by suggesting that they would be missing important potential health benefits if they do not agree to allow unlimited access to their genome data. Some even go so far as to threaten that this will hamper Aboriginal peoples’ future development in relation to health benefits. This argument represents an underlying paternalistic attitude and is at odds with the United Nations Declaration on the Rights of Indigenous Peoples, which holds that Indigenous people own their own data and information.

The attitudes of such scientists have set back DNA studies in Australia. Future researchers will need to overcome this, and establish working partnerships with Aboriginal people. Such partnerships should ultimately result in benefits to both groups. In the longer term, this is more important than any one scientific achievement.

My interactions with the three tribal groups of the Willandra Lakes region and other Indigenous communities across Australia took place over the course of a decade. These have led to joint authorship on major publications that have resolved issues of Indigenous interest and empowered Aboriginal Australians themselves. Our publication of the eighty-three complete genomes of Aboriginal people included the following Aboriginal authors: Les Murgha, Thomas Wales, Betty Logan, Warren Clark, Doc Reynolds, Gudjugudju Fourmile, Darren Injle, Aubrey Lynch and Colleen Wall.

Finally, the long-term goal of this research is the training of Indigenous Australians. This is of fundamental importance. This kind of research needs to be undertaken and led by emerging Indigenous researchers. At a more general level, this will in turn enable the further breaking down of barriers between scientific and Indigenous knowledge.


From Griffith Review Edition 60: First Things First © Copyright Griffith University & the author.

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