Research activities at the Australian Centre for Ancient DNA(ACAD)

Identifying the remains of missing persons, either natural mortalities or victims of murder, natural disaster, terrorism, wars and/or humanitarian violations, is a growing global issue with significant social, legal and cultural impacts. Recent terrorist attacks (World Trade Centre, Bali Bombings) and natural disasters (south east Asian tsunami, Victorian bushfires) have focused national and international attention on the problem of Disaster Victim Identification. However unidentified natural mortalities and murder victims represent a "silent mass disaster" (~40,000 sets of unidentified human remains in the USA). Similarly, forced disappearances (civilians kidnapped and murdered by their own governments) and armed conflicts have resulted in the disappearance of hundreds of thousands of people over the last century and future demand for the genetic analysis of mass graves is predicted to grow dramatically. 

Contact Dr Jeremy Austin

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 (see Conservation Paleontology section).

Contact: Professor Alan Cooper

 

 

Contact: Dr Jeremy Austin

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: Dr Wolfgang Haak

The advent of genomics technology such as Next Generation Sequencing technologies has revolutionised the ancient DNA field. Recent studies of the complete genomes of the Neandertal and Denisova specimens have catapulted the field into the area of genomics. Fortunately, most of the current genomic sequencing platforms can only work with short fragments of DNA (from 30-500bp), which is exactly the range found in ancient specimens. In addition to standard sequencing approaches, ACAD has pioneered the application of single Nucleotide Polymorphism (SNP) chips to ancient DNA, to rapidly assay>50,000 genetic polymorphisms instantly. Preliminary work on ancient bovids has recently been published (Decker et al. 2010), and currenlty a major research promgram is underway to develop and authoenticate the use of SNP chips for a variety of aDNA studies, including humans, bovids, and other animal and plant species, including several domestic species.

Contact: Professor Alan Cooper

ACAD, in collaboration with the Environment Institute and Australian Genome Research Facility (AGRF), was recently awarded funding from Bioplatforms Australia (BPA) to purchase and establish the first 3rd Generation Sequencing platform in Australia. This technology permits the anlaysis of single molecules of DNA in real-time, avoiding the need for prior amplification of templates. This technology has major advantages for the accurate measurement of both ancient and environmental samples, where the frequency and sequence of alleles is often altered during the amplification process. Currently, ACAD is working closely with Pacific Biosciences to adapt their SMRT technology for ancient and museum specimens, as well as for a variety of forensics applications. This partnership has involved exchange of pre-commerical proprietary technology, and some of the first analyses of ancient specimens using 3rd Generation sequencing.

Contact: Professor Alan Cooper

One of the main over-arching themes of ACAD research is Conservation Paleontology, where detailed studies of the past evolutionary and ecological processes are used to improve our understanding of current conservation priorities, to improve managmenet and planning. This research ranges from the genetic identification of extinct species and population to guide reintroduction programs (eg. Victorian bettongs), to in-depth analyses of the responses of populations to environmental changes (such as climatic or human impacts) over time. ACAD uses both museum specimens and samples recovered from remote field sites around the world (from Siberia to Patagonia) to reconstruct past environments, and how they have changed through time. These studies have identified a remarkably strong influence of climate change on the biodiversity and distribution of large vertebrates over the past 100,000 years (such as brown bears, bison, horses, lions, NZ moa). Indeed, the biological responses to past climatic events typically appear to be so dynamic and complex that genetic anlayses of living populations (in the absence of ancient DNA data) appear unlikely to accurately reconstruct evolutionary history. Similar studies of Australian biota have revealed marked signals of past climatic impacts, and highlight potentially concerning issues for the long-term stability of many Australian environments. This is a pressing area for current research. Conservation Paleontology will be one of the key priority research areas for ACAD over the next 5 years, and a new centre for Conservation Paleontological research is currenlty in development.

Contact: Professor Alan Cooper