Research Activities at ACAD
ACAD is one of the leading ancient DNA centres in the world, and with an international reputation for highly-innovative research is developing new platform technolgies and collaborative programs with international research leaders across multiple fields. Expertise at ACAD is catagorised in several major areas/themes.
ACAD has been awarded several million dollars worth of research funding from the Australian Research Council (ARC), State and Federal Government agencies since establishing in 2005, and has several linkages with international collaboroators and museums. We greatly appreciate the support of the ARC and our Business Partners for our continued research endeavours:
ACAD has invested in high powered computing capacity to develop in-house pipelines and algorythms for bioinformatics capabilities. Aided by our annual international bioinformatics workshops, our team is acquiring skills and work on the latest software for the analysis of Next Generation Sequencing (NGS), Genomics and Metagenomics data, including tools and methods to handle NGS and SNP array data. Contact Bastien Llamas.
DNA based human identification is both critical and central to criminal and coronial investigations, disaster-victim and missing persons identification, repatriation of war dead and counter-terrorism operations. ACAD's Advanced Forensic unit is developing and applying a novel targeted sequence capture and high throughput DNA sequencing approach to simultaneously type thousands of informative identity, ancestry and phenotype markers in a single assay to idenfity suspects/missing persons. You can read more on our forensic work here.
The reconstruction of the human evolutionary history is the focal point of a wide range of scientific disciplines including human biology, human genetics, medical sciences, archaeology and palaeo-anthropology. It is essential to understand the underlying mechanisms of how humans adapt when encountering new environmental challenges (many of which can be man-made), when facing climatic changes (e.g. the last glacial maximum), or when undergoing changes in subsistence strategies (i.e. from a hunter-gatherer to a farming lifestyle). How much of the human adaptability can be ascribed to classical biological adaptation of the organism (via natural selection) vs. general plasticity of the human physiology and vs. the ability to tackle challenges through cultural and behavioural flexibility? Similarly, what evolutionary forces shape genes that are involved in response to the ever-present exposure to pathogens or that contribute to the risk of human disease given a particular lifestyle/environment? In addition, uni-parental markers (mtDNA and Y-chromosome) allow the reconstruction of phylogenetic relatedness and therefore allow us to track past migrations and describe pre-(historic) expansion patterns.Ancient DNA approaches provide a direct temporal perspective to studies on human evolution, allowing genetic change and diversity to be tracked through time and linked to cultural and environmental events documented in the archaeological and geological records. This approach has enabled long-standing questions such as the advent and spread of farming to be addressed and solved through the analysis of ancient populations. Our research addresses major questions in human evolutionary biology, which centre on human interactions and response to environment, climate change and disease during the peopling of all continents, and aims to reconstruct the evolutionary processes that have shaped modern-day human diversity accessing high-resolution genomic information from a well-selected range of prehistoric human DNA samples from diverse sources (hair, bone, teeth, dental calculus, coprolites etc). Contact Professor Alan Cooper or Dr Bastien Llamas.
Using ancient bacterial DNA obtained from calcified dental plaque (calculus) and Next Generation Sequencing technologies, we are actively investigating the evolution of the human microbiome to understand how long-term changes in the microbiome impact health and disease. Using ancient samples obtained from around the word that date back to 55,000 years ago, we ask how microorganisms establish themselves in the human body, understanding how diverse bacterial communities are formed under different selection regimes, i.e. environment, diet, culture, and disease. Our aim is to examine how different microbiomes, established through different evolutionary histories, impact our ability to fight infectious disease, in ancient, modern, westernized, Indigenous human, Neandertal and primate populations around the world. Our research team is also analysing whole bacterial genome evolution in real-time, investigating the selection pressures that drive bacterial evolution in diversity microbial communities. To read more about this research, please see our Nature Genetics article (Adler et al, 2013, Sequencing ancient calcified dental plaque shows changes in oral microbiota with dietary shifts of the Neolithic and Industrial revolutions. Nature Genetics 45:450-455) Contact Laura Weyrich.
ACAD has published a number of ground-breaking studies in the genetic analysis of megafaunal extinctions during the Late Quaternary (last 2 Ma), principally in the Late Pleistocene where both genetic and climatic records are most developed. This research uses DNA sequences from ancient bone, teeth, mummified tissues, and even sediments from specimens around the world to reconstruct the history of populations and ecosystems overtime. New research is utilising bacterial sequences and stable isotope signals to complement these records. These genetic records have revealed major transitions (extinctions, invasions, genetic bottlenecks) and changes in population size and diversity that are generally hidden from the standard fossil record. Analyses on large vertebrate populations in the Holarctic (brown bears, lions, horses, bovids, humans etc) and southern hemisphere (moa, camelids, marsupials) have revealed a surprisingly dynamic picture of repeated extinctions, replacements and migrations in response to climatic changes, and human impacts. Concerningly, the results suggest that studies of modern populations alone would be unlikely to accurately reconstruct the evolutionary and paleoecological history, and may have generated an inaccurate picture of the biological consequences of environmental change. This is an important concern, given that most modern conservation and ecological studies are based on the analysis of such short-term records. Contact Alan Cooper.
A recently funded project from the Australian Research Council (2012) aims to study what role past climate changes have played in both driving the diversification and extinction of terrestrial faunas. Using powerful new genomics and analytical methods on tissue samples held in Australian museums, the research will construct a comprehensive genetic record of the past climate change during the Last Glacial Maximum (around 20,000 years ago) on Australian native animals. This information will determine which species and ecosystems were most adversely impacted by rapid climate change and why, and the extent of loss of biodiversity and range shifts. New climate models developed from this information will be key to understanding the resilience of Australian ecosystems, and managing existing populations to minimise the impact of current climatic trends.