DNA reveals Aboriginal people had a long and settled connection to country

Historic hair samples collected from Aboriginal people show that following an initial migration 50,000 years ago, populations spread rapidly around the east and west coasts of Australia.

Our research, published in Nature today, also shows that once settled, Aboriginal groups remained in their discrete geographical regions right up until the arrival of Europeans a few hundred years ago.

So where does the evidence for this rapid migration and long settlement come from?

Early expeditions

In a series of remarkable expeditions that ran from the 1920s to 1960s, scientists travelled widely across the Australian outback. They recorded as much anthropological information as possible about Aboriginal Australians.

They recorded film and audio, drawings, songlines, genealogies and extensive physical measurements under tough outback conditions. This included packing in the equipment on camels for the early trips.

Alan Rau, EO Stocker and Herbert Wilkinson on an expedition party departing for a day’s trip from Cockatoo Creek, Central Australia, 1931. South Australian Museum Archives Norman Tindale Collection (AA 338/5/7/8), Author provided

The extensive collections from the Board for Anthropological Expeditions are now curated in the South Australian Museum. They contain the vast majority of the black and white film footage you may have seen of traditional Aboriginal culture, songs, hunting practices and ceremonies.

The metadata collected was voluminous. It now comprises possibly the best anthropological collection of an indigenous people in the world.

Locked in the hair

But perhaps the biggest scientific contributions may yet turn out to be hidden within small locks of hair.

These were collected with permission (such as it was given in the situation and era) for a minor project to study the variation of Aboriginal hair types across Australia.

But the hair clippings turn out to preserve an incredible record of the genetic diversity and distribution of Indigenous Australia prior to European disruption.

Importantly, the detailed genealogical data collected with each sample allows the genetic lineages to be placed on the map back through several generations.

This allowed us to reconstruct the genetic structure within Australia prior to the forced relocation of Aboriginal people to missions and stations, sometimes thousands of kilometres from their traditional lands.

Reconnecting histories

This project was only possible through partnership with Aboriginal families and communities. So we needed to design an ethical framework and protocol for such unprecedented work.

This was based on large amounts of archival research performed by our team members in the Aboriginal Family History Unit of the South Australian Museum, to locate and contact the original donors, or their descendants and family elders.

We arranged a meeting time, and then the combined team spent several days in each Aboriginal community talking to individual families about the project, and passing on copies of the archival material.

We discussed both the potential and pitfalls of genetic research, and answered common questions. These included why the results cannot be used for land claim issues (insufficient geographical resolution) or as a test of Aboriginality (which is a cultural, rather than genetic, association).

The feedback from communities was overwhelmingly positive. There was a strong interest in how a genetic map of Aboriginal Australia could help people of the stolen generation to reconnect with family and country.

It could also help facilitate the repatriation of Aboriginal samples and artefacts held in museums.

The DNA results

The initial genetic results not only reveal exciting insights into the deep genetic history of the continent, but also showcase the enormous potential of our project.

We mapped the maternal genetic lineages onto the birthplace of the oldest recorded maternal ancestor (sometimes two to three generations back) and found there were striking patterns of Australia’s genetic past.

There were many very deep genetic branches, stretching back 45,000 to 50,000 years. We compared these dates to records of the earliest archaeological sites around Australia. We found that the people appear to have arrived in Australia almost exactly 50,000 years ago.

Early migration

Those first Australians entered a landmass we collectively call “Sahul”, where New Guinea was connected to Australia.

The Gulf of Carpentaria was a massive fresh water lake at the time and most likely a very attractive place for the founding population.

The genetic lineages show that the first Aboriginal populations swept around the coasts of Australia in two parallel waves. One went clockwise and the other counter-clockwise, before meeting somewhere in South Australia.

The occupation of the coasts was rapid, perhaps taking no longer than 2,000 to 3,000 years. But after that, the genetic patterns suggest that populations quickly settled down into specific territory or country, and have moved very little since.

The genetic lineages within each region are clearly very divergent. They tell us that people – once settled in a particular landscape – stayed connected within their realms for up to 50,000 years despite huge environmental and climate changes.

We should remember that this is about ten times as long as all of the European history we’re commonly taught.

This pattern is very unusual elsewhere in the world, and underlines why there might be such remarkable Aboriginal cultural and spiritual connection to land and country.

As Kaurna Elder, Lewis O’Brien, one of the original hair donors and part of the advisory group for the study, put it:

Aboriginal people have always known that we have been on our land since the start of our time, but it is important to have science show that to the rest of the world.

Reprint from The Conversation

The First Human Epidemic: Late Pleistocene Origin?

Current models of infectious disease in the Pleistocene tell us little about the pathogens that would have infected Neanderthals (Homo neanderthalensis). High quality Altai Neanderthal and Denisovan genomes are revealing which regions of archaic hominin DNA have persisted in the modern human genome. A number of these regions are associated with response to infection and immunity, with a suggestion that derived Neanderthal alleles found in modern Europeans and East Asians may be associated with autoimmunity. Independent sources of DNA-based evidence allow a re-evaluation of the nature and timing of the first epidemiologic transition. The paradigm of the first epidemiologic transmission, the hypothesis that epidemic disease did not occur until the transition to agriculture, with larger, denser and more sedentary populations, has been essentially unchallenged since the 1970s. Our views of the infectious disease environment of the Pleistocene period are heavily influenced by skeletal data and studies of contemporary hunter-gatherers. New genetic data – encompassing both hosts and pathogens – has the power to transform our view of the infectious disease landscape experienced by Neanderthals in Europe, and the anatomically modern humans (AMH) with whom they came into contact. The Pleistocene hominin environment cannot be thought of as free from infectious disease. It seems likely that the first epidemiologic transition, envisaged as part of the package of the Holocene farming lifestyle, may be fundamentally different in pace or scope than has previously been suggested. This paper demonstrates how high quality genomic data sets can be used to address questions arisingfrom the ecological context that shaped the co-evolutionary relationship we share with infectious diseases. We analyse the evidence for infectious disease in Neanderthals, beginning with that of infection-related skeletal pathologies in the archaeological record, and then consider the role of infection in hominin evolution. We have synthesised current models on the chronology of emergence of notable European disease packages and analyse what implications this evidence has for the classical model of the first epidemiologic transition. Using emerging data from Neanderthal palaeogenomics and combining this with fossil and archaeological information we re-examine the impact of infectious diseases on human populations from an evolutionary context. These palaeogeneticists argue that the first epidemiologic transition in Eurasia was not as tightly tied to the onset of the Holocene as has previously been assumed. There is clear evidence to suggest that this transition began before the appearance of agriculture and occurred over a timescale of tens of thousands of years. We suggest that the epidemiological transition was not, as has been thought since the 1970s, a phenomenon of the human shift to sedentary agriculture during the Holocene but a much older and more complex process that involved at least two species of humans. The origin of resistance to infectious disease has a much deeper timeframe and is highlighted by the ingression of Neanderthal DNA into modern human lineages. The transfer of pathogens between human species may also have played a role in the extinction of the Neanderthals. Our analysis of the genomes of archaic hominins provides evidence of pathogens acting as a population-level selection pressure, causing changes in genomes that were passed on to descendants and preserved in the genomes of modern Eurasians. the analysis of ancient genomes demonstrates that human behavioural patterns (in this case a shift to agricultural subsistence) should not be used as an ecological proxy to explain shifting trends in the co-evolutionary relationship between pathogens and human populations.

This work is available on BioRxiv: http://dx.doi.org/10.1101/017343

Acknowledgements: Rob Foley, Marta Lahr and the members of the Human Evolutionary Science Discussion Group at the University
of Cambridge. Funding for this research was provided by King’s College Cambridge and UCL.

Homo floresiensis: Extracting Ancient Deoxyribonucleic Acid (aDNA): It’s Been 4 Years, any success?

I recently came across this scientific article in the Journal of Human Evolution entitled, Ancient DNA Analysis of Dental Calculus by Weyrich et al. It reminded me of the research conducted on the Indonesian hominin, Homo floresiensis. So, here I summarise what we know thus far. Dating to between 95,000 and 17,000 years ago, the hominin was found in the cave of Liang Bua, overlooking the Wae Racang river valley, on the island of Flores. It’s most remarkable feature was the 1.06 m stature of the individual found. Begging the question, how is this hominin related to us and what led to its diminutive stature. Much of the debate was thoroughly summarised in Leslie Aiello’s paper entitled, Five Years of Homo floresiensis, back in 2010. In short, some questioned the validity of naming these individuals a new species of human. Evidence was brought forward to support the hypothesis that these people were suffering from the neurodevelopmental disorder, Microcephaly and other diseases that induce a reduced stature. As time has passed, media sensation abated and researchers had a chance to step back, the majority are now more accepting of the Australian-Indonesian team’s decision to apply the new hominin nomenclature. Much of the debate hinges on skeletal comparisons between Homo floresiensis and other hominins, like us. There is one piece of information that the individuals of Liang Bua have yet to reveal – Deoxyribonucleic Acid.

Kilimutu Crater Lakes, Flores, Indonesia
Kilimutu Crater Lakes, Flores, Indonesia

Two teams of scientists, the Australian Centre for Ancient DNA (ACAD) and the Department of Evolutionary Anthropology at the Max Planck Institute (MPI) attempted and failed to extract DNA from the individual’s teeth in 2006. This was due to the environment in which the hominins were found, which was not conducive to DNA preservation. Christina Adler of ACAD hypothesised that the reason for extraction failure could be due to extraction procedure. In 2007 the ACAD team sucessfully extracted DNA from a pig tooth unearthed at the Liang Bua Cave, which was about 6,000 years old. The team suggested that first, Cementum (calcified root covering) is the richest source of DNA and second, drilling the specimen destroys the very molecule they are after. Armed with this knowledge another attempt to extract DNA from the hominins of Liang Bua is still yet to be carried out. The year 2013, saw the successful extraction of 400,000 year old DNA in Spain, so Floresiensian DNA may still lie within the teeth. I’m hoping, despite the less than ideal high temperatures of the cave sediments, there lies within those hominin individuals such strands of the good stuff.

Cranium and mandible cast of Homo floresiensis individual, LB1
Cranium and mandible cast of Homo floresiensis individual, LB1

Returning to the paper I mentioned at the beginning, it is a summary of all we know regarding the extraction of aDNA and steps to take when extracting it from calculus on teeth. Calculus is a hardened group of micro-organisms that appear as a yellow build-up usually around the gum-tooth boundary. The first demonstration of aDNA in Calculus was documented in a paper entitled Ancient Bacterial DNA (aDNA) in dental calculus from archaeological human remains by Preus et al., in 2011. A year later, aDNA was extracted from Neolithic Argentinian and Chilean humans. In that study, five bacterial species gene sequences were amplified by targeted polymerase chain reactions (PCR). By 2014, Warinner et al., used the power of the metagenomic sequencing strategy demonstrated increased resolution, the identification of antibiotic resistence genes and though the specimens were put through an Ethylenediaminetetraacetic acid (EDTA) and bleach treatments, DNA was recoverable.

Deoxyribonucleic Acid (DNA)
Deoxyribonucleic Acid (DNA)

When analysing hominin diets, microfossils are a large component, but the strides being made in aDNA extraction will mean that the species of plant or animal will be identified or as it usually does, throws up more questions than answers.

The Joys of Science!

Social Media Destinations:

Facebook: https://www.facebook.com/charlesgfclarke

Twitter: https://twitter.com/Cennathis

Google+: https://plus.google.com/113974359890947358730/posts

WordPress: https://cennathis.com/

Tumblr: https://www.tumblr.com/blog/cennathis

Academia.edu: https://ucl.academia.edu/charlestgclarke

SoundCloud: https://soundcloud.com/charlestgclarke