Murdoch University ancient DNA research laboratory

In 1984, the first published ancient DNA (aDNA) sequence was based on the extraction and sequencing of 229 base pairs of mitochondrial DNA (mtDNA) from the extinct quagga, Equus quagga (Higuchi et al. 1984). Two decades later, and following the invention of polymerase chain reaction (PCR), aDNA sequence data are applied in many fields, including; climate change, biodiversity, extinctions, taxonomy, conservation, anthropology, and molecular evolution. It is the goal of this lab's research to first assess the long-term survival DNA under Australian conditions and second, to use aDNA sequence data to answer a multitude of biological questions both in Australia and elsewhere.

DNA degrades post-mortem at a rate that depends on many environmental factors – eventually reaching the point where no authentic DNA can be recovered. Historically aDNA studies have focused on samples obtained from frozen or “cool” environments because temperature was thought to be the single most important factor in the survival of DNA. The prevalence of high and fluctuating temperatures, and extreme ranges of humidity, have meant that warm climates, such as Australia, have been largely dismissed as a place where aDNA techniques can be applied. In fact, some studies predict that such environments are so hostile to DNA preservation that it should not survive for more than a few years. However, these predictions are proving unreliable as authentic aDNA has been extracted from from middens, coprolites and sediments in arid desert environments in the South-Western USA (Hofreiter et al. 2000, 2003, Kuch et al. 2003 and Poinar et al. 2003). Only recently has the field started to explore the chemistry of preservation and begun to formulate techniques capable of extracting aDNA from samples/environments that were previously thought to be inimical to long-term DNA survival.

For a good review of ancient DNA see: (www.eva.mpg.de/primat/files/pdfs/PaaboARG2004.pdf)

Paabo, S., Poinar, H., Serre, D., Jaenicke-Despres, V., Hebler, J., Rohland, N., Kuch, M., Krause, J., Vigilant, L., and Hofreiter, M. (2004). Genetic analyses from ancient DNA. Annu Rev Genet 38, 645-679.

Why are ancient DNA sequences useful? DNA sequences from "old" biological samples can be used to answer a variety of questions including:

- Evolutionary history of extinct species (e.g. Dodo's and Mammoths)

- Human origins (e.g. Neanderthal DNA)

- Measuring past biodiversity including extinction timing and causes (e.g. Bison)

- Taxonomic resolution (e.g. New Zealand Moa)

- Ancient Pathogen DNA (e.g. 1918 flu and early HIV strains)

- Study of molecular evolution (the use of phylogenetics to understand the tempo and mode of evolution)

- Species Identification (where only bone fragments, coprolites or  hair have survived)

- Ecosystem reconstructions (what species used to live there? - what species is best to reintroduce?)

- Midden Analysis (use DNA profiles to determine diet and how it changed over time).

- Environmental reconstructions (using DNA profiles from sediments to determine the composition of past ecosystems)

The middens of the Lesser and Greater Stick-nest Rats (Leporillus apicalis; L. conditor) are widespread across arid zones in Australia. Both species are now extinct on mainland Australia, but L. conditor survives on West and Eastern Franklin Islands off South Australia- and has been successfully introduced onto a few others. These rodents assemble remarkable (up to 1m high and 1.5m in diameter) nests of sticks, that become middens composed of sticks and plant and animal remains (Watts and Eves, 1976), cemented together by the viscous urine, which solidifies into a hard substance known as amberat. Dating shows that some nest/midden sites have been used continuously for centuries (Webeck and Pearson, 2005). The middens do not just include rat and plant remains because both species of Leporillus scavenged material from throughout their home ranges; nests contain bone, egg shell, hair, faecal matter of bats, echidnas, dingos, owls, insects and other species (Pearson and Dodson, 1993). The middens therefore represent a legacy of material from the environment at the time of deposition. Traditional macroscopic analysis (pollen profiling), and carbon dating have allowed researchers to investigate the history of Australia’s arid zones. DNA profiling of has been used to study the middens of American desert rodents (Kuch et al., 2002) and giant ground sloths (Poinar et al., 2003), and is an excellent way of investigating the former ranges of extinct and endangered species and how their diets may have changed through time. A major research program on fossil American pack-rat middens has, over 25 years, provided unparalleled spatial and temporal information on late Quaternary climates and ecological change in arid and semi-arid environments (Van Devender and Spaulding, 1979). Arguably, at the moment this is the richest archive of dated, identified, and well-preserved plant and animal remains in the world (Pearson and Betancourt, 2002). 

Preliminary data from middens (dating 700-4000 years-old) from Queensland, New South Wales and Western Australia demonstrate that DNA survives in these deposits and can be extracted and amplified when appropriate methodologies are employed. One research project that will be running in the lab over the next few years is to investigate DNA preservation (using qPCR) and use DNA profiling to reconstruct what plants, animals and insects were living in these past environments. It is hoped the middens will act as a genetic "time capsule" to investigate the past ecosystems.

80 million years ago the landmass that constitutes New Zealand separated from the southern “super-continent” called Gondwana.  Following the extinction of dinosaurs 65 million years ago New Zealand did not “follow” the evolutionary path of other landmasses, in that birds rather than mammals became the dominant herbivore. Prior to human settlement 700 years ago New Zealand had no terrestrial mammals  - apart from three species of bats - instead approximately 250 avian species dominated the ecosystem half of which are now extinct.

The lack of mammals is thought to of prompted the evolution of many flightless birds, the most striking of which is the herbivorous moa (pictured) - approximately 10 species of which lived in different habitats in New Zealand's North and South Island (pictured). Moa were ill-adapted to deal with the introduction of humans and rodents, and were driven to extinction about 500-800 years ago. 

Human males have an X and a Y chromosome, whereas females are XX, therefore the DNA on the Y chromosome can positively identify DNA as being male.  Researchers have employed a similar approach with ancient moa DNA to identify the sex of moa bones (Bunce et al. 2003 and Huynen et al. 2003) - this research was some of the first use of ancient nuclear DNA to determine characteristics of extinct fauna.  The data conclusively demonstrated that females were substantially larger than males (up to 3 times the mass), a phenomenon known as reversed sexual dimorphism. The image on this page compares an averaged sized male and female with a pigeon as a scale. Research using ancient DNA and isotopes to understand the taxonomy, evolutionary history and diet is ongoing. In 2006 we secured a 3 year Marsden grant (for $825,000) to AMS 14C date and profile (with stable isotopes and DNA) moa from two North Canterbury swamps. The goal of the research is to increase our understanding of moa ecology and the environment which they occupied.

Among other extinction events in New Zealand was the Haast's eagle (Harpagornis moorei). Haast’s eagle (10-15kg, 2-3 m wingspan) (Holdaway 1994) was 30-40% heavier than the largest extant eagle (the Harpy eagle,) and hunted moa up to 15 times its weight (pictured). In a dramatic example of morphological plasticity and rapid size increase, we show that the Haast’s Eagle was not related to the Australian wedge-tailed eagle but very closely related the world’s smallest extant eagles (the Australian Little Eagle), approximately 1/10th its mass. This spectacular evolutionary change illustrates the potential speed of size alteration within lineages of vertebrates, especially in island ecosystems.

From time to time the lab will have research projects (and possibly funding) for PhD, Masters and Honours students. These projects will be listed here. Unfortunately the lab is  unable to take on all the students that are interested in working in the lab - there is simply not the space or resources. Prospective students are encouraged to do some background research into the kind of research (and methodologies) that are conducted in the field of ancient DNA labs before making contact with the lab. Information about Murdoch University scholarships can be found here: http://www.research.murdoch.edu.au/gradcentre/scholar.html 

Sept 2007

I am interested in recruiting an Australian student with an APA to start a PhD in the lab in 2008 on a project to recover DNA from Australian samples (bone, middens and sediments). If you are interested in studying in this area please contact Mike Bunce for more details (contact information can be found here). A pdf of potential projects can be found here.