A description of what our lab does (click here for larger image)
DNA audits of TCMs - click on the image below or here to watch some video footage
Aboriginal DNA provides human migration clues - ABC news
New Aboriginal genome - some comments from the authors
On a Wing and a Prayer Trailer - Cockatoo story featuring Nicole White
Dr Mike Bunce Talks about ancient eggshell DNA on the BBC.
The staining of DNA within the fossil eggshell of the extinct Moa.
aDNA images: The extinct moa and eagle (John Megahan) and examples of samples used for aDNA analyses; mummified Dodo, moa bone and a 10,000 year old Australian coprolite ("poo")
Welcome to the Murdoch University Ancient DNA Research Lab website. The lab is located in Perth, Western Australia. The purpose of this website is to promote the research that the lab undertakes and to provide information about our research activites to the public, collaborators and prospective students.
Don't know what ancient DNA is? then click here.
The website content falls into the following five categories and is best navigated using the tabs above.
Personal in our labs run a non profit wildlife forensics service that offers species identification and DNA profiling services to the Australian community. Details about these services can be located at www.wildlifeforensics.com.au
Some recent (and not so recent) laboratory "news and highlights" that you might want to know about:
(October 2012) Understanding DNA decay.
A better understanding of long-term DNA decay has been achieved after studying 158 fossilised leg bones belonging to three species of the moa.
Dr Morten Allentoft (a former post-doc in the lab now in Copenhagen) used dated bones between 600 and 8000 years old to calculate that, for a 242 bp fragment, DNA has a half-life of 521 years. The estimated rate is almost 400 times slower than predicted from simulation experiments carried out in the lab.
Time since deposition accounted for approximately 39% of the variation so other factors are clearly at play (fossil storage, soil chemistry and microbial attack).
The research can be used to better model DNA decay - and using the new estimate it reaffirms, at least for bone, Jurassic park is a pipe-dream as even under frozen conditions the last two bases of DNA would break at approximately 6.8 million years.
coverage:
www.newscientist.com/article/dn22359-dnas-halflife-identified-using-fossil-bones.html
www.nature.com/news/dna-has-a-521-year-half-life-1.11555
Mike Bunce talks about the research on Triple J - listen here.
(April 2012) The genetic audit of 15 Traditional Chinese Medicines using next-generation sequencing.
TCMs have a long cultural history but today, consumers need to be aware of the legal and health safety issues before adopting them as a treatment option.
Fifteen TCM samples, seized by border officials, in the form of powders, tablets, capsules, flakes and herbal teas were audited using the DNA preserved in the samples. This work is part of Megan Coghlan's PhD project to build a molecular toolkit for wildlife forensic applications. The results are published in the journal PLoS Genetics.
In total Meghan found 68 different plant families in the medicines – they are complex mixtures of species. Some of the TCMs contained plants of the genus Ephedra and Asarum. These plants contain chemicals which can be toxic if the wrong dosage is taken, but none of them actually listed concentrations on the packaging
Traces from trade restricted animals that are classified as vulnerable, endangered, or critically endangered, including the Asiatic black bear and Saiga antelope were also detected.
Until now it has been difficult to determine the biological origins of ingredients contained within TCMs because processing into pills and powders makes identification difficult.
It is hoped that this new approach to genetically audit medicinal products will bring about a new level of regulation to the area of complementary and alternative medicine.
Some videos on the left sidebar explain the findings. the article can be found at: http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1002657
(September 2011) The complete genome of an Aboriginal Australian reconstructed from a 100 year-old lock of hair.
In an exciting development, an international team of scientists including researchers from Murdoch University have, for the first time, pieced together the human genome from an Aboriginal Australian. The results, now to be published in the international journal Science, reinterpret world prehistory.
By sequencing the genome, the researchers demonstrate that Aboriginal Australians descend directly from an early human expansion into Asia that already took place some 70,000 years ago, at least 24,000 years before the population movements that gave rise to present day Europeans and Asians. The results imply that modern day Aboriginal Australians are in fact the direct descendents of the first people who arrived on the continent by 50,000 years ago.
The study derived from a lock of hair donated to a British anthropologist by an Aboriginal man from the Goldfields region of Western Australia in the early 20th century. One hundred years later, researchers have isolated DNA from this same hair, using it to explore the genetics of the first Australians and to provide insights into how humans first dispersed across the globe.
Some YouTube videos on the left sidebar explain the findings. the article can be found at: http://www.sciencemag.org/content/333/6050/1689
(April 2011) The evolutionary History of cockatoos.
Cockatoos are native to the Australian region but are now found all over the globe as aviary pets due to their colourful plumage, charismatic nature and capacity for learning.
Murdoch University researchers have used new DNA sequencing techniques to help give them a better understanding of how cockatoo species have evolved and how they fit together in a family tree.
Nicole White, who carried out the research, said some of the findings were surprising. For example, some species of cockatoo which look quite different were actually closely related.
“A large black cockatoo known as the palm cockatoo was found to cluster on the family tree with the white cockatoos, rather than with the other blacks. Likewise the relationship between the gang-gang (which has a red head and a black body) and galah (pink head and body with grey wings) was shown to be closer than previously thought,” said Nicole.
“So just because some cockatoos might look similar, this doesn’t necessarily mean they are closely related.
The research has been published in the journal: Molecular Phylogenetics and Evolution.
http://www.abc.net.au/science/articles/2011/04/05/3181871.htm
http://www.cosmosmagazine.com/node/4240/full
(March 2010) The recovery of ancient DNA from Eggshell .
Fossil eggshells are frequently recovered from deposits across the globe and have been extensively used as a tool for radiocarbon dating and as a proxy to study past environments. Charlotte Oskam et al. have shown for the first time that ancient DNA is preserved with in the matrix of fossil eggshell. Some more information can be found at the following links:
http://www.nature.com/news/2010/100310/full/news.2010.111.html
http://news.bbc.co.uk/2/hi/8558683.stm
An audio file (MP3) from a BBC interview can be found on this webpage.
(February 2010) The first ever ancient human complete genome
Our lab was part of an international research team, led by Professor Eske Willerslev at the University of Copenhagen, isolated and sequenced the DNA from a 4000 year old clump of male hair found during an archaeological excavation in Greenland. The team spent the best part of a year isolating the DNA assembling the DNA blue-print known as a genome.
Analysis of the genes of the pre-historic Greenlander, know as the Saqqaq, have provided new insights into how the Eskimo, looked – including his tendency to baldness, brown eyes, dark skin, shovel-shaped front teeth and dry earwax, the DNA sequence also showed Saqqaq had blood type A+ and was genetically adapted to cold temperatures.
This kind of research heralds a new era of archaeology and shows how small fragments of hair and bone stored in museum collections can provide exciting new ways of studying human history.
click here to listen to a 20min mp3 audio file (~9 MB) where one of the team members A/Prof Tom Gilbert discusses this research on Radio New Zealand News.
Moa ancient DNA provides insights into New Zealand past
DNA recovered from remains of the moa, a giant extinct bird, have revealed a surprising new geological history of New Zealand says a study published by Bunce et al. (2009) in the Proceeding of the National Academy of Sciences (see publications). After almost being totally submerged 25 million years ago, the current North and South islands were separated by a large sea until around 1.5 million years ago, during which time most of the famous New Zealand species survived and evolved just on the South Island.
New Zealand is recognized as one of the world’s great ‘evolutionary laboratories’ due to the absence of land mammals and the radiations of giant flightless birds such as the moa and our most recent research used morphology, geology, carbon dating and ancient DNA in combination to
Sept 2007: Isolating DNA from 1/2 million year old bacteria: PNAS paper. Exactly how bacterial cells can survive for thousands of years, encapsulated in ice, amber and other materials has been the subject of much debate. The predominant hypothesis is that the cells are dormant enabling them to survive harsh conditions. But such dormancy usually stops metabolism, including DNA repair. Without constant maintenance the genome is vulnerable to chemical reactions that damage the DNA. Eventually cells accumulate so much damage that the reproduction is not possible.
Bacterial samples sealed in Siberian permafrost that has been undisturbed for more than half a million years were collected and analysed. The researchers amplified long pieces of DNA and measured the respiration of the ancient cells to determine if they were alive. Johnson et al. detected metabolic activity in ice samples up to 600,000 yeas old and reveal that the key to the longevity of these bacteria is continuous DNA repair. The authors suggest that permafrost environments around the world may harbor species of viable bacteria adapted to past environments. They also raise the point that similar life detection strategies might be employed on ice from Mars or Europa to investigate if these environments ever harbored life.
For more information check out the article at the PNAS website
and the following web link to a story at ABC online
July 2007: Greenland aDNA paper published in Science: Our lab was part of an international research team (lead by Prof Eske Willerslev) that was published in Science. The research showed that DNA from sediments under the Greenland icecap, dating back more than 450,000 years, – was once inhabited by a diverse array of conifer trees and insects. The research is fascinating as it demonstrates that preserved DNA from plants, animals, insects and bacteria that died hundreds of thousands of years ago can aid in our understanding of how the earth’s environment has changed over time. See news item in the Sydney Morning Herald:
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